wgEncodeBroadHmm Broad ChromHMM GSE38163 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation  Note: these data have been converted via liftOver from the Mar. 2006 (NCBI36/hg18) version of the track. Description This track displays a chromatin state segmentation for each of nine human cell types. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input CTCF, H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K9ac, H3K36me3, H4K20me1, H3K27me3, and Input Control --> using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. GM12878 - lymphoblastoid cells H1-ESC - embryonic stem cells HepG2 - hepatocellular carcinoma HUVEC - Human Umbilical Vein Endothelial Cell HMEC - Human Mammary Epithelial Cells HSMM - Normal Human Skeletal Muscle Myoblasts K562 - erythroleukemia cells NHEK - Normal Human Epidermal Keratinocytes NHLF - Normal Human Lung Fibroblasts --> Display Conventions and Configuration This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different cell type and displays individually on the browser. Instructions for configuring tracks with multiple subtracks are here. The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows: State 1 -  Bright Red  - Active Promoter State 2 -  Light Red  -Weak Promoter State 3 -  Purple  - Inactive/poised Promoter State 4 -  Orange  - Strong enhancer State 5 -  Orange  - Strong enhancer State 6 -  Yellow  - Weak/poised enhancer State 7 -  Yellow  - Weak/poised enhancer State 8 -  Blue  - Insulator State 9 -  Dark Green  - Transcriptional transition State 10 -  Dark Green  - Transcriptional elongation State 11 -  Light Green  - Weak transcribed State 12 -  Gray  - Polycomb-repressed State 13 -  Light Gray  - Heterochromatin; low signal State 14 -  Light Gray  - Repetitive/Copy Number Variation State 15 -  Light Gray  - Repetitive/Copy Number Variation Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq data from the Broad Histone track was used to generate this track. Data for nine factors plus input and nine cell types was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted). Release Notes This is release 1 (Jun 2011) of this track. It was lifted over from the NCBI36/hg18 version of the track, and is therefore based on the NCBI36/hg18 release of the Broad Histone track. It is anticipated that the HMM methods will be run on the newer datasets in the GRCh37/hg19 version of the Broad Histone track, and, once that happens, the new data will replace this liftOver. Credits The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School, and the chromatin state segmentation was produced in Manolis Kellis's Computational Biology group at the Massachusetts Institute of Technology. Contact: Jason Ernst. Data generation and analysis was supported by funds from the NHGRI (ENCODE), the Burroughs Wellcome Fund, Howard Hughes Medical Institute, NSF, Sloan Foundation, Massachusetts General Hospital and the Broad Institute. References Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. There is no restriction on the use of segmentation data. 
wgEncodeHistoneSuper ENC Histone ENCODE Histone Modification Regulation Description These tracks display maps of chromatin state of ENCODE cell types. Histones are a group of closely-related proteins that together form the nucleosome. There are six histone families: H1, H2A, H2B, H3, H4, and H5. Each nucleosome core is formed by two H2A-H2B dimers and a H3-H4 tetramer, while H1 and H5 bind the nucleosome and DNA. When histone proteins undergo post-transcriptional modifications at specific amino acids (methylation, acyetylation), these modifications (referred to as marks) perform a role in regulating the winding of the DNA around the nucleosome. This in turn regulates gene expression by controlling the accessibility of the chromatin. Histone marks vary in their effect. Promoters, enhancers, transcribed regions, and silenced regions are each associated with specific histone marks. The ChIP-seq method enables identifying regions of DNA that interact with specific histone marks. This method involves cross-linking histones and other DNA associated proteins to genomic DNA within cells using formaldehyde. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. This has the effect of capturing segments of DNA that are bound to the protein selected by the antibody. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. If the antibody is specific to a given histone mark, then this procedure identifies segments of the genome associated with that mark. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87(2):117-25. Segal E, Widom J. What controls nucleosome positions? Trends Genet. 2009 Aug;25(8):335-43. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeBroadHmmNhlfHMM NHLF ChromHMM NHLF Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000792 792 GSM936086 Bernstein Broad hg18 ChromHMM_ENCODEDynamicPaper wgEncodeBroadHmmNhlfHMM HMM lung fibroblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHLF Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmNhekHMM NHEK ChromHMM NHEK Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000791 791 GSM936087 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmNhekHMM HMM epidermal keratinocytes Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHEK Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHsmmHMM HSMM ChromHMM HSMM Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000787 787 GSM936085 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHsmmHMM HMM skeletal muscle myoblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HSMM Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHmecHMM HMEC ChromHMM HMEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000786 786 GSM936084 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHmecHMM HMM mammary epithelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HMEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHuvecHMM HUVEC ChromHMM HUVEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000788 788 GSM936089 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHuvecHMM HMM umbilical vein endothelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HUVEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHepg2HMM HepG2 ChromHMM HepG2 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000789 789 GSM936090 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHepg2HMM HMM hepatocellular carcinoma Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HepG2 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmK562HMM K562 ChromHMM K562 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000790 790 GSM936088 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmK562HMM HMM leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model K562 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmH1hescHMM H1-hESC ChromHMM H1-hESC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000785 785 GSM936083 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmH1hescHMM HMM embryonic stem cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model H1-hESC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmGm12878HMM GM12878 ChromHMM GM12878 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000784 784 GSM936082 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmGm12878HMM HMM B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model GM12878 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHistone Broad Histone 2012-06-30 GSE29611 Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation Description This track displays maps of chromatin state generated by the Broad/MGH ENCODE group using ChIP-seq. Chemical modifications (methylation, acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views: Peaks Regions of statistically significant signal enrichment. The score associated with each enriched interval is the mean signal value across the interval. (Note that a broad region with moderate enrichment may deviate from the background more significantly than a short region with high signal.) Signal Density graph (wiggle) of signal enrichment. At each base-pair position, the density is calculated as the number of sequenced tags overlapping a 25 bp window centered at that position. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq: Cells were grown according to the approved ENCODE cell culture protocols. Cells were fixed in 1% formaldehyde and resuspended in lysis buffer. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibodies against each of the histone antibodies listed above. Antibody-chromatin complexes were pulled down using protein A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, treated with RNAse and purified. A quantity of 1-10 ng of DNA was end-repaired, adapter-ligated and sequenced by Illumina Genome Analyzers as recommended by the manufacturer. Alignment: Sequence reads from each IP experiment were aligned to the human reference genome (GRCh37/hg19) using MAQ with default parameters, except '-C 11' and '-H output_file' were added. These options output up to 11 additional best matches for each read (if any are found) to a file. This information was used to filter out any read that had more than 10 best matches on the genome. Note that it is likely that instances where multiple reads align to the same position and with the same orientation are due to enhanced PCR amplification of a single DNA fragment. No attempt has been made, however, to remove such artifacts from the data, following ENCODE practices. Signal: Fragment densities were computed by counting the number of reads overlapping each 25 bp bin along the genome. Densities were computed using igvtools count with default parameters (in particular, '-w 25' to set window size of 25 bp and '-f mean' to report the mean value across the window), except for '-e' which was set to extend the reads to 200 bp, and the .wig output was converted to bigWig using wigToBigWig from the UCSC Kent software package. Peaks: Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal. All data sets were processed with '-task chip', and with '-windows 100,200,500,1000,5000,10000,100000' (no mask file nor the '-trim' option have been used). The resulting called segments were then further filtered to remove intervals that were significantly enriched only because they contain smaller enriched intervals within them. This post-processing step has been implemented using Matlab. The use of the post-processing step allowed very large enriched intervals (of the order of Mbps for H3K27me3, for instance) to be detected, as well as much smaller intervals, without the need to tailor the parameters of Scripture based on prior expectations. Release Notes This is Release 3 (Aug 2012). It contains 83 new experiments including 6 new cell lines and 25 new antibodies. Please note that an antibody previously labeled "Pol2 (b)" is, in fact, Covance antibody MMS-128P with the target POLR2A. Credits The ChIP-seq data were generated at the Broad Institute and in the Bernstein lab at the Massachusetts General Hospital/Harvard Medical School.    Data generation and analysis were supported by funds from the NHGRI, the Burroughs Wellcome Fund, Massachusetts General Hospital and the Broad Institute. Contact: Noam Shoresh References Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ 3rd, Gingeras TR et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28;120(2):169-81. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21;125(2):315-26. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May;28(5):503-10. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 2;448(7153):553-60. Publications Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23;147(7):1628-39. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until, above. The full data release policy for ENCODE is available here. 
wgEncodeBroadHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoblControlStdSig Osteobl Input Input Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001056 1056 GSM733697 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblControlStdSig None Signal osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoP300kat3bSig Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneOsteoP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Sig Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Sig Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdSig Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Sig Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdSig Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdSig Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Sig Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneOsteoH3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal Osteoblasts H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdSig Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdSig Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdSig Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdSig Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfControlStdSig NHLF Input Input NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000105 105 GSM733731 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfControlStdSig None Signal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdSig NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Sig NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdSig NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdSig NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdSig NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Sig NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdSig NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdSig NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdSig NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdSig NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azSig NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Sig NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdSig NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekControlStdSig NHEK Input Input NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000072 72 GSM733740 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekControlStdSig None Signal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdSig NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdSig NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Sig NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdSig NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdSig NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdSig NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdSig NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Sig NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdSig NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdSig NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdSig NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdSig NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azSig NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Sig NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdSig NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadControlStdSig NHDF-Ad Input Input NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001055 1055 GSM733750 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadControlStdSig None Signal adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Sig NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Sig NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdSig NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdSig NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdSig NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Sig NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdSig NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdSig NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdSig NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Sig NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azSig NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneNhdfadH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal NHDF-Ad H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Sig NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdSig NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaControlStdSig NH-A Input Input NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001027 1027 GSM733678 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaControlStdSig None Signal astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Sig NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Sig NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdSig NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdSig NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdSig NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Sig NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acSig NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdSig NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Sig NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdSig NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azSig NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Sig NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdSig NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtControlStdSig HSMMtube Input Input HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001001 1001 GSM733648 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtControlStdSig None Signal skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdSig HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdSig HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdSig HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Sig HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneHsmmtH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal HSMMtube H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdSig HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Sig HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdSig HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdSig HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdSig HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdSig HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdSig HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Sig HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHsmmtEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdSig HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmControlStdSig HSMM Input Input HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000119 119 GSM733663 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmControlStdSig None Signal skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdSig HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdSig HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdSig HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdSig HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdSig HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdSig HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdSig HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdSig HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdSig HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdSig HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdSig HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Sig HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdSig HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecControlStdSig HMEC Input Input HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000093 93 GSM733668 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecControlStdSig None Signal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdSig HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Sig HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdSig HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdSig HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdSig HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Sig HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdSig HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdSig HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdSig HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdSig HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azSig HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Sig HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdSig HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-27 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41ControlStdSig Dnd41 Input Input Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002434 2434 GSM1003558 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41ControlStdSig None Signal T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Sig Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Sig Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Sig Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Sig Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acSig Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Sig Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acSig Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Sig Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Sig Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Sig Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azSig Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Sig Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfSig Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746ControlSig CD14+ Control Control Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003130 3130 GSM1003475 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746ControlSig None Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ Control Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acSig CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acSig CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K4me2 Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azSig CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfSig CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecControlStdSig HUVEC Input Input HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000060 60 GSM733715 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecControlStdSig None Signal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdSig HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdSig HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Sig HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdSig HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-26 2009-01-06 2009-10-06 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdSig HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdSig HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdSig HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Sig HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdSig HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdSig HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdSig HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdSig HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azSig HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Sig HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdSig HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2ControlStdSig HepG2 Input Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000084 84 GSM733732 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2ControlStdSig None Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdSig HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdSig HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdSig HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdSig HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdSig HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Sig HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHepg2H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HepG2 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdSig HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdSig HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdSig HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdSig HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdSig HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Sig HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdSig HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3ControlStdSig HeLa-S3 Input Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001013 1013 GSM733659 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3ControlStdSig None Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdSig HeLa-S3 Pol2(b) Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Pol2(b) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdSig HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdSig HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdSig HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdSig HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdSig HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Sig HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdSig HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdSig HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdSig HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdSig HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azSig HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Sig HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHelas3Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdSig HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Sig CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acSig CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Sig CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ControlSig CD20+ Control Control CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003132 3132 GSM1003477 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ControlSig None Signal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Sig CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azSig CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfSig CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlEtoh02Sig A549 EtOH Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003076 3076 GSM1003541 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlEtoh02Sig EtOH_0.02pct Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlDex100nmSig A549 DEX Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003075 3075 GSM1003540 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlDex100nmSig DEX_100nM Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Sig A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H4k20me1Etoh02Sig EtOH_0.02pct Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Sig A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Etoh02Sig EtOH_0.02pct Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmSig A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Dex100nmSig DEX_100nM Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Sig A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Etoh02Sig EtOH_0.02pct Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmSig A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Dex100nmSig DEX_100nM Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Sig A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmSig A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Dex100nmSig DEX_100nM Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Sig A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmSig A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acDex100nmSig DEX_100nM Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Sig A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Sig A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Sig A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp wgEncodeBroadHistoneA549H3k04me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmSig A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me3Dex100nmSig DEX_100nM Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Sig A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Etoh02Sig EtOH_0.02pct Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmSig A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Dex100nmSig DEX_100nM Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Sig A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Etoh02Sig EtOH_0.02pct Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmSig A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Dex100nmSig DEX_100nM Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Sig A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azEtoh02Sig EtOH_0.02pct Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmSig A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azDex100nmSig DEX_100nM Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Sig A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfEtoh02Sig EtOH_0.02pct Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmSig A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfDex100nmSig DEX_100nM Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562ControlStdSig K562 Input Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000052 52 GSM733780 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562ControlStdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Sig K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Suz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Sig K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Sirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Sig K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Setdb1Sig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SETDB1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdSig K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Sap3039731StdSig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Sig K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Rnf2Sig None Signal Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 RNF2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestSig K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562RestSig None Signal A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 REST Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdSig K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Rbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdSig K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdSig K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Plu1StdSig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdSig K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Phf8a301772aStdSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafSig K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562PcafSig None Signal PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 PCAF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdSig K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562P300StdSig None Signal EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 P300 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Sig K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Nsd2ab75359Sig None Signal This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 NSD2 (ab75359) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorSig K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562NcorSig None Signal The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 NCoR Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Sig K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Lsd1Sig None Signal BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 LSD1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aSig K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdSig K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac2a300705aStdSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdSig K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac1sc6298StdSig None Signal Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdSig K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdSig K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdSig K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdSig K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdSig K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdSig K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdSig K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdSig K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdSig K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdSig K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdSig K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdSig K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdSig K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Ezh239875StdSig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdSig K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Sig K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Chd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Sig K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Chd4mi2Sig None Signal CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CHD4 Mi2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdSig K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Chd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Sig K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx8Sig None Signal CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX8 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Sig K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbx3sc101004Sig None Signal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Sig K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx2Sig None Signal Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Sig K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbpsc369Sig None Signal CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBP (sc-369) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescControlStdSig H1-hESC Input Input H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000088 88 GSM733770 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescControlStdSig None Signal embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Sig H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSuz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Sig H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Sig H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSap3039731Sig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Sig H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPlu1Sig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aSig H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPhf8a301772aSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bSig H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig None Signal JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdSig H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescJarid1aab26049StdSig None Signal Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aSig H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aSig H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac2a300705aSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdSig H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdSig H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdSig H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdSig H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdSig H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdSig H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k09me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdSig H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdSig H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdSig H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdSig H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-30 2010-06-30 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdSig H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Sig H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneH1hescEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdSig H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Sig H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescChd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdSig H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescChd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878ControlStdSig GM12878 Input Input GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH000037 37 GSM733742 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878ControlStdSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdSig GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdSig GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdSig GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdSig GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdSig GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdSig GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-04 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdSig GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdSig GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Sig GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdSig GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoP300kat3bPk Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Pk Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Pk Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdPk Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Pk Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdPk Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdPk Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Pk Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment Osteoblasts H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdPk Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdPk Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdPk Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdPk Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdPk NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Pk NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdPk NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdPk NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdPk NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Pk NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdPk NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdPk NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdPk NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdPk NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azPk NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Pk NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdPk NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdPk NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdPk NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Pk NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdPk NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdPk NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdPk NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdPk NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Pk NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdPk NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdPk NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdPk NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdPk NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azPk NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Pk NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdPk NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Pk NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Pk NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdPk NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdPk NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdPk NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Pk NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdPk NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdPk NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdPk NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Pk NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azPk NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment NHDF-Ad H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Pk NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdPk NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Pk NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Pk NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdPk NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdPk NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdPk NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Pk NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acPk NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdPk NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Pk NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdPk NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azPk NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Pk NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdPk NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdPk HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdPk HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdPk HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Pk HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment HSMMtube H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdPk HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Pk HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdPk HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdPk HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdPk HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdPk HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdPk HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Pk HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdPk HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdPk HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdPk HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdPk HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdPk HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdPk HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdPk HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdPk HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdPk HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdPk HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdPk HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdPk HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Pk HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdPk HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdPk HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Pk HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdPk HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdPk HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdPk HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Pk HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdPk HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdPk HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdPk HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdPk HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azPk HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Pk HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdPk HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Pk Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Pk Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Pk Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Pk Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acPk Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Pk Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acPk Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Pk Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Pk Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Pk Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azPk Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Pk Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfPk Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acPk CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acPk CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azPk CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfPk CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdPk HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdPk HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Pk HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdPk HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-12 2011-05-05 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdPk HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdPk HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdPk HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Pk HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdPk HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdPk HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdPk HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdPk HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azPk HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Pk HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdPk HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdPk HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdPk HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdPk HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdPk HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdPk HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Pk HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HepG2 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdPk HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdPk HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdPk HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdPk HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdPk HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Pk HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdPk HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdPk HeLa-S3 Pol2 Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdPk HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdPk HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdPk HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdPk HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdPk HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Pk HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdPk HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdPk HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdPk HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdPk HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azPk HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Pk HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdPk HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Pk CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acPk CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Pk CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Pk CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azPk CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfPk CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Pk A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H4k20me1Etoh02Pk EtOH_0.02pct Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Pk A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Etoh02Pk EtOH_0.02pct Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmPk A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Dex100nmPk DEX_100nM Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Pk A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Etoh02Pk EtOH_0.02pct Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmPk A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Dex100nmPk DEX_100nM Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Pk A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmPk A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Pk A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmPk A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acDex100nmPk DEX_100nM Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Pk A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Pk A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Pk A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmPk A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Pk A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Etoh02Pk EtOH_0.02pct Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmPk A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Dex100nmPk DEX_100nM Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Pk A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Etoh02Pk EtOH_0.02pct Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmPk A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Dex100nmPk DEX_100nM Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Pk A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azEtoh02Pk EtOH_0.02pct Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmPk A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azDex100nmPk DEX_100nM Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Pk A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfEtoh02Pk EtOH_0.02pct Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmPk A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfDex100nmPk DEX_100nM Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Pk K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Suz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Pk K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Pk K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Setdb1Pk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SETDB1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdPk K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sap3039731StdPk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Pk K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rnf2Pk None Peaks Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 RNF2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestPk K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562RestPk None Peaks A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 REST Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdPk K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdPk K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdPk K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Plu1StdPk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdPk K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Phf8a301772aStdPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafPk K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562PcafPk None Peaks PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 PCAF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdPk K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562P300StdPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 P300 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Pk K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Nsd2ab75359Pk None Peaks This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 NSD2 (ab75359) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorPk K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562NcorPk None Peaks The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 NCoR Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Pk K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Lsd1Pk None Peaks BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 LSD1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aPk K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdPk K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac2a300705aStdPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdPk K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac1sc6298StdPk None Peaks Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdPk K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdPk K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdPk K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdPk K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdPk K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdPk K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdPk K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdPk K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdPk K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdPk K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdPk K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdPk K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdPk K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Ezh239875StdPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdPk K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Pk K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Pk K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd4mi2Pk None Peaks CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CHD4 Mi2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdPk K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Pk K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx8Pk None Peaks CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX8 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Pk K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx3sc101004Pk None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Pk K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx2Pk None Peaks Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Pk K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbpsc369Pk None Peaks CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBP (sc-369) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Pk H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSuz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Pk H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Pk H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSap3039731Pk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Pk H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPlu1Pk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aPk H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPhf8a301772aPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bPk H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk None Peaks JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdPk H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJarid1aab26049StdPk None Peaks Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aPk H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aPk H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac2a300705aPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdPk H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdPk H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdPk H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdPk H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdPk H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdPk H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k09me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdPk H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdPk H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdPk H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdPk H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdPk H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Pk H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdPk H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Pk H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdPk H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdPk GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdPk GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdPk GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdPk GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdPk GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdPk GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdPk GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdPk GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Pk GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdPk GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeCaltechRnaSeq Caltech RNA-seq GSE33480 RNA-seq from ENCODE/Caltech Expression Description This track was produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-seq was performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done on an Illumina Genome Analyzer (GAI or GAIIx) (Mortazavi et al., 2008). The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA using two different protocols: one that preserves information about which strand the read is coming from and one that does not. Due to the specifics of the enzymology of library construction, gene and transcript quantification is more accurate based on the non-strand-specific protocol, while the strand-specific protocol is useful for assigning strandedness, but in general less reliable for quantification. Non-strand-specific Protocol (deep "reference" transcriptome measurements, 2x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis, converted into cDNA by random priming and then amplified. Data were produced in two formats: single reads, each of which came from one end of a cDNA molecule, and paired-end reads, which were obtained as pairs from both ends of cDNAs. This RNA-seq protocol does not specify the coding strand. As a result, there is ambiguity at loci where both strands are transcribed. The "randomly primed" reverse transcription is, apparently, not fully random. This is inferred from a sequence bias in the first residues of the read population, and this likely contributes to observed unevenness in sequence coverage across transcripts. Strand-specific Protocol (1x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis. A set of 3' and 5' adapters were ligated to the 3' and 5' ends of the fragments, respectively. The resulting RNA molecules were converted to cDNA and amplified. This RNA-seq protocol does specify the coding strand as each read is in the same 5'-3' orientation as the original RNA strand. As a result, loci where both strands are transcribed can be disambiguated. However, RNA ligation is an inherently biased process and as a result, greater unevenness in sequence coverage across transcripts is observed compared to the non-strand-specific data, and quantification is less accurate. Data Analysis Reads were aligned to the hg19 human reference genome using TopHat (Trapnell et al., 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo. Cufflinks (Trapnell et al., 2010), a de novo transcript assembly and quantification software package, was run on the TopHat alignments to discover and quantify novel transcripts and to obtain transcript expression estimates based on the GENCODE annotation. All sequence files, alignments, gene and transcript models and expression estimates files are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Alignments The Alignments view shows reads aligned to the genome. Alignments are colored by cell type. The tags used in this file are: NH XS CP NM CC. The 'XS' custom tag indicates the sense/anti-sense of the strand. See the Bowtie Manual (Langmead et al., 2009) for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. For Stranded Data (1x75) Plus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the forward strand. Minus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the reverse strand. Minus strand score is multiplied by -1 for display purposes so that data can be viewed around an axis. For Paired-End Non-Stranded Data (2x75) Raw Signal (only for paired-end data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). The RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. A separate track for the forward (plus) and reverse (minus) strands are provided for strand-specific data. Splice Sites Subset of aligned reads that crosses splice junctions. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols except for H1-hESC for which frozen cell pellets were purchased from Cellular Dynamics. Cells were lysed in RLT buffer (Qiagen RNeasy kit) and processed on RNeasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. A quantity of 75 µg of total RNA was selected twice with oligo-dT beads (Dynal) according to the manufacturer's protocol to isolate mRNA from each of the preparations. For 2x75 bp non-stranded RNA-seq, 100 ng of mRNA was then processed according to the protocol in Mortazavi et al. (2008), and prepared for sequencing on the Genome Analyzer flow cell according to the protocol for the ChIP-seq DNA genomic DNA kit (Illumina). The majority of paired-end libraries were size-selected around 200 bp (fragment length) with the exception of a few additional replicates that were size-selected at 400 bp with the specific intent to investigate the effect of fragment length on results. Strand-specific RNA-seq libraries were prepared from 100 ng of mRNA from the same preparation following Illumina's Strand-Specific RNA-seq protocol. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Reads of 75 bp length were obtained, single-end for directional, strand-specific libraries (1x75D) and paired-end for non-strand-specific libraries (2x75). Data Processing and Analysis Reads were mapped to the reference human genome (version hg19), with or without the Y chromosome, depending on the sex of the cell line, and without the random chromosomes and haplotypes in all cases, using TopHat (version 1.0.14). TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance. After mapping reads to the genome and identifying splice junctions, the data were further analyzed using the transcript assembly and quantification software Cufflinks (version 0.9.3) using the sequence bias detection and correction option. Cufflinks was used in two modes: 1) expression for genes and individual transcripts was quantified based on the GENCODE annotation, for both versions v3c and v4 of GENCODE GRCh37; 2) Cufflinks was run in de novo transcript assembly and quantification mode to obtain candidate novel transcript and gene models and expression estimates for them. Downloadable Files The following files can be found on the downloads page: .fastq - Raw sequence files in fastq format with phred33 quality scores. Junctions.bedRnaElements - A BED file containing TopHat-defined splice junctions. TranscriptDeNovo.gtf - A GTF file containing transcript models and expression estimates in FPKM (Fragments Per Kilobase per Million reads) produced by Cufflinks in de novo mode. TranscriptGencV3c.gtf - Expression level estimates at the transcript level for the GENCODE GRCh37.v3c annotation in GTF format. GenesDeNovo.gtf - Expression estimates for genes defined by Cufflinks in de novo mode in GTF format. GeneGencV3c.gtf - Expression level estimates at the gene level for the GENCODE GRCh37.v3c annotation in GTF format. ExonGencV3c.gtf - Expression level estimates for GENCODE GRCh37.v3c exons in GTF format derived by summing the expression levels in FPKM for all transcripts containing a given exon. TSS.gtf - Expression level estimates for GENCODE GRCh37.v3c transcription start sites (TSS) in GTF format derived by summing the expression levels in FPKM for all transcripts originating from a given TSS. Verification Known exon maps as displayed on the genome browser are confirmed by the alignment of sequence reads. Known spliced exons are detected at the expected frequency for transcripts of given abundance. Linear range detection of spiked-in RNA transcripts from Arabidopsis and phage lambda over 5 orders of magnitude. Endpoint RT-PCR confirms presence of selected 3' UTR extensions. Correlation to published microarray data r = 0.62. Release Notes This is release 4 (August 2012). Fastq files for GM12892, GM12891 and K562 (R1x75) were replaced after errors were found in the GEO submission process. Credits Wold Group: Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Brandon King, Ken McCue, Lorian Schaeffer. Myers Group: Norma Neff, Florencia Pauli, Fan Zhang, Tim Reddy, Rami Rauch, Chris Partridge. Illumina gene expression group: Gary Schroth, Shujun Luo, Eric Vermaas. TopHat/Cufflinks development: Cole Trapnell, Lior Pachter, Steven Salzberg. Contacts: Georgi Marinov (data coordination/informatics/experimental), Diane Trout (informatics) and Brian Williams (experimental). References Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRnaSeqSuper ENC RNA-seq ENCODE RNA-seq Expression Description RNA sequencing, or RNA-seq, is a method for mapping and quantifying the total amount of RNA transcripts in a cell at any given time, otherwise known as the transcriptome, for any organism that has a genomic DNA sequence assembly. Compared to microarrays that detect and quantify transcripts by hybridization against known sequences, RNA-seq directly sequences transcripts and is especially well-suited for de novo discovery of RNA splicing patterns and for determining unequivocally the presence or absence of lower abundance class RNAs. RNA-seq is performed by reverse-transcribing an RNA sample into cDNA followed by high throughput DNA sequencing. Most data is produced in the format of either single reads or paired-end reads. In the format of single reads each sequence read comes from one end of a randomly primed cDNA molecule (and represent one end of one cDNA segment), while paired-end reads are obtained as pairs from both ends of a randomly primed cDNA (and represent two opposite ends of one cDNA segment). The resulting sequence reads are then informatically mapped onto the genome sequence (Alignments). The current mappers (TopHat and STAR) have the ability to map reads to annotated and unannotated genomic regions. Reads mapped to annotated or novel RNA splice junctions are (Splice Sites). Earlier versions of this software did not map reads to unannotated genomic regions. Some RNA-seq protocols do not specify the coding strand. As a result, there can be ambiguity at loci where both strands are transcribed. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics. 2009;10:135-51. Metzker ML. Sequencing technologies - the next generation. Nature Reviews: Genetics. 2010 Jan;11(1):31-46 Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeCaltechRnaSeqViewSplices Splice Juctions RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 NHLF 2x75 Sp 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 NHLF 2x75 Sp 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 NHEK 1x75D Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 NHEK 2x75 Sp 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 NHEK 2x75 Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 HSMM 2x75 Sp 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 HSMM 2x75 Sp 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 HCT6 2x75 Sp 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 HCT6 2x75 Sp 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 GM92 2x75 Sp 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 GM92 2x75 Sp 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 GM92 2x75 Sp 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 GM91 2x75 Sp 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 GM91 2x75 Sp 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 MCF7 2x75 Sp 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 MCF7 2x75 Sp 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 MCF7 2x75 Sp 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 LHCND 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 DIFF_7d Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Subset of aligned reads that cross splice junctions LHCN-M2 Myocyte 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 LHCN 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions LHCN-M2 Myoblast 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 HUVEC 1x75D Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 HUVEC 1x75D Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 HUVEC 2x75 Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 HUVEC 2x75 Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 HepG 1x75D Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 HepG 1x75D Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 HepG 2x75 Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 HepG 2x75 Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 HeLa 1x75D Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 HeLa 1x75D Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 HeLa 2x75 Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 HeLa 2x75 Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 K562 1x75D Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 K562 1x75D Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 K562 2x75 Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 K562 2x75 Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 H1ES 1x75D Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 H1ES 1x75D Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 H1ES 400 Sp 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 400 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 H1ES 2x75 Sp 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 H1ES 2x75 Sp 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 H1ES 2x75 Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 H1ES 2x75 Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 GM78 1x75D Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 GM78 1x75D Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 GM78 400 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 400 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 GM78 2x75 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 GM78 2x75 Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewSignal Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 NHLF 2x75 Sg 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 NHLF 2x75 Sg 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 NHEK 2x75 Sg 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 NHEK 2x75 Sg 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 HSMM 2x75 Sg 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 HSMM 2x75 Sg 1 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 HCT6 2x75 Sg 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 HCT6 2x75 Sg 1 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 GM92 2x75 Sg 3 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 GM92 2x75 Sg 2 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 GM92 2x75 Sg 1 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 GM91 2x75 Sg 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 GM91 2x75 Sg 1 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 MCF7 2x75 Sg 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 MCF7 2x75 Sg 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 MCF7 2x75 Sg 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 LHCND 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 DIFF_7d Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Signal LHCN-M2 Myocyte 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 LHCN 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal LHCN-M2 Myoblast 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 HUVEC 2x75 Sg 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 HUVEC 2x75 Sg 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 HepG 2x75 Sg 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 HepG 2x75 Sg 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 HeLa 2x75 Sg 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 HeLa 2x75 Sg 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 K562 2x75 Sg 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 K562 2x75 Sg 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 H1ES 400 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 400 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 H1ES 2x75 Sg 4 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 H1ES 2x75 Sg 3 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 H1ES 2x75 Sg 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 H1ES 2x75 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 GM78 400 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal GM12878 400 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 GM78 2x75 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 GM78 2x75 Sg 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewPlusSignal Plus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 NHEK 1x75D + 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 PlusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand NHEK single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 HUVEC 1x75D + 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 HUVEC 1x75D + 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 HepG 1x75D + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 HepG 1x75D + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 HeLa 1x75D + 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 HeLa 1x75D + 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 K562 1x75D + 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 K562 1x75D + 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 H1ES 1x75D + 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 H1ES 1x75D + 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 GM78 1x75D + 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 GM78 1x75D + 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewMinusSignal Minus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 NHEK 1x75D - 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 MinusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand NHEK single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 HUVEC 1x75D - 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 HUVEC 1x75D - 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 HepG 1x75D - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 HepG 1x75D - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 HeLa 1x75D - 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 HeLa 1x75D - 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 K562 1x75D - 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 K562 1x75D - 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 H1ES 1x75D - 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 H1ES 1x75D - 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 GM78 1x75D - 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 GM78 1x75D - 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewAligns Alignments RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 NHLF 2x75 A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 NHLF 2x75 A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 NHEK 1x75D A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 NHEK 2x75 A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 NHEK 2x75 A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 HSMM 2x75 A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 HSMM 2x75 A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 HCT6 2x75 A 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 HCT6 2x75 A 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 GM92 2x75 A 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 GM92 2x75 A 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 GM92 2x75 A 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 GM91 2x75 A 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 GM91 2x75 A 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 MCF7 2x75 A 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001421 1421 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 MCF7 2x75 A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 MCF7 2x75 A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 LHCND 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 DIFF_7d Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myocyte 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 LHCN 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myoblast 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 HUVEC 1x75D A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 HUVEC 1x75D A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 HUVEC 2x75 A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 HUVEC 2x75 A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 HepG 1x75D A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 HepG 1x75D A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 HepG 2x75 A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 HepG 2x75 A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 HeLa 1x75D A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 HeLa 1x75D A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 HeLa 2x75 A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 HeLa 2x75 A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 K562 1x75D A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 K562 1x75D A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 K562 2x75 A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 K562 2x75 A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 H1ES 1x75D A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 H1ES 1x75D A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 H1ES 400 A 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 400 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 H1ES 2x75 A 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 H1ES 2x75 A 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 H1ES 2x75 A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 H1ES 2x75 A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 GM78 1x75D A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 GM78 1x75D A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 GM78 400 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 400 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 GM78 2x75 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 GM78 2x75 A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCshlLongRnaSeq CSHL Long RNA-seq GSE30567 Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression Description These tracks were generated by the ENCODE Consortium. They contain information about human RNAs greater than 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform. Data are available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, there are also data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, see the RIKEN CAGE Loc track), Small RNA-seq (less than 200 nucleotides, see the CSHL Sm RNA-seq track) and Pair-End di-TAG-RNA (PET-RNA, see the GIS RNA PET track) datasets available from the same biological replicates. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Contigs The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates. Specific column specifications can be found in the supplemental directory. Signals The Plus Signal and Minus Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively. Alignments The Alignments view shows individual reads mapped from biological replicates to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format. See the SAM Format Specification for more information on the SAM/BAM file format. Splice Junctions Subset of aligned reads that cross splice junctions. Specific column specifications can be found in the supplemental directory. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Additional views are available on the downloads page. Methods Cell Culture Cells were grown according to the approved ENCODE cell culture protocols. Library Preparation The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The Illumina PhiX control library was also spiked-in at 1% to each completed human library just prior to cluster formation. Accompanying each RNA-seq dataset is a Protocol document available for download as a PDF. This document contains details about the RNA isolations and treatments, library construction, spike-ins as well as quality control figures for individual libraries. The spike-in sequence and the concentrations are available for download in the supplemental directory. Sequencing and Mapping The libraries were sequenced on the Illumina GAIIx platform as paired-ends for 76 or 101 cycles for each read. The average depth of sequencing was ~200 million reads (100 million paired-ends). The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab. For each experiment there are additional element data views data files available for download. These elements were assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to use as a threshold. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the sum of the bioreplicates is 90%. In addition, expression values for annotated genes, transcripts and exons were computed. Further explanation of these files is available for download in the supplemental directory. Verification FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated Gencode exons and Spearman values were compared. In general, Rho values are greater than .90 between biological replicates. Release Notes This is release 3 (Sept 2012) of this track for hg19. It has no new experiments, but has additional files for many experiments. The hMNC-CB experiment has been revoked. The doubly compressed spike-ins files have been uncompressed. The hMNC-PB experiment has been replaced with improved depth. The current downloadable elements files (Transcripts, Genes and Exons) were generated using GENCODE V10, while the older datasets were generated using GENCODE V7. The "view" metadata will specify V7 or V10 for these files. Errata 6/6/2013 - CSHL reports that one lane of reads is missing from the SK-N-SH-RA fastq read2 file (wgEncodeCshlLongRnaSeqSknshraCellPapFastqRd2Rep1.fastq.gz). Credits These data were generated and analyzed by the transcriptome group led by Tom Gingeras at Cold Spring Harbor Laboratories and the laboratory of Roderic Guigo at the Center for Genomic Regulation (CRG) in Barcelona. Contact: Carrie Davis References Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. Publications Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep;22(9):1658-67. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Sep 5;13(9):R53. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeCshlLongRnaSeqViewJunctions Splice Junctions Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapJunctions SKRA cel pA+ J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamJunctions SKRA cel pA- J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions SkMC cel tot J SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions Junctions Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SkMC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapJunctions NHLF cel pA+ J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamJunctions NHLF cel pA- J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions NHMM2 cel tot J NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions Junctions Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions NHMf cel tot J NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions Junctions Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM.f M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions NHEK nuc pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions NHEK nuc pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions NHEK cyt pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions NHEK cyt pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapJunctions NHEK cel pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamJunctions NHEK cel pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions NHDF cel tot J NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions Junctions Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHDF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalJunctions HWP cel tot J HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalJunctions Junctions Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HWP whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions HVMF cel tot J HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions Junctions villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HVMF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapJunctions HSMM cel pA+ J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamJunctions HSMM cel pA- J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions HSVEC cel tot J HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions Junctions Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSaVEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions HPIEC cel tot J HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions Junctions Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPIEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions HPCPL cel tot J HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions Junctions Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPC-PL whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalJunctions HOB cel tot J HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalJunctions Junctions Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HOB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions hMSUC cel tot J hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-UC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions hMSBM cel tot J hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-BM whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions hMSAT cel tot J hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-AT whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 hMNPB cel tot J hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 Junctions Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMNC-PB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions HMEpC cel tot J HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions Junctions Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapJunctions HMEC cel pA+ J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamJunctions HMEC cel pA- J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions HFDPC cel tot J HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions Junctions Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HFDPC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalJunctions HCH cel tot J HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalJunctions Junctions Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HCH whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions HAoEC cel tot J HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions Junctions Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions HAoAF cel tot J HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions Junctions Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoAF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions CD34 cel tot J CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions Junctions hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD34+ Mobilized whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapJunctions BJ cel pA+ J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamJunctions BJ cel pA- J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapJunctions AG50 cel pA+ J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamJunctions AG50 cel pA- J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions SKNSH nuc pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions SKNSH cyt pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapJunctions SKNSH cel pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions CD14 cel pA+ J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions CD14 cel pA- J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions MCF7 nuc pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions MCF7 cyt pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapJunctions MCF7 cel pA+ J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamJunctions MCF7 cel pA- J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions IMR90 nuc pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions IMR90 cyt pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalJunctions IMR90 cel tot J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapJunctions IMR90 cel pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions HUVEC nuc pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions HUVEC nuc pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions HUVEC cyt pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions HUVEC cyt pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapJunctions HUVEC cel pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamJunctions HUVEC cel pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions HeG2 nuc pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions HeG2 nuc pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions HeG2 cyt pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions HeG2 cyt pA- J HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapJunctions HeG2 cel pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamJunctions HeG2 cel pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions HeS3 nuc pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions HeS3 nuc pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions HeS3 cyt pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions HeS3 cyt pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapJunctions HeS3 cel pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamJunctions HeS3 cel pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapJunctions CD20 cel pA+ J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamJunctions CD20 cel pA- J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapJunctions A549 nuc pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapJunctions A549 cyt pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapJunctions A549 cel pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamJunctions A549 cel pA- J A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapJunctions K562 nuc pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamJunctions K562 nuc pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions K562 ncpm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleoplasm total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapJunctions K562 cyt pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamJunctions K562 cyt pA- J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions K562 chrm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 chromatin total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapJunctions K562 cel pA+ J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamJunctions K562 cel pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions H1hSC nuc pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions H1hSC nuc pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions H1hSC cyt pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions H1hSC cyt pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapJunctions H1hSC cel pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamJunctions H1hSC cel pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions GM78 nuc pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions GM78 nuc pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions GM78 nlus tot J GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleolus total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions GM78 cyt pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions GM78 cyt pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapJunctions GM78 cel pA+ J GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamJunctions GM78 cel pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewPlusSig Plus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 SKRA cel pA+ + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 SKRA cel pA+ + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 SKRA cel pA- + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 SKRA cel pA- + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 SkMC cel tot + 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 SkMC cel tot + 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 NHLF cel pA+ + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 NHLF cel pA+ + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 NHLF cel pA- + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 NHLF cel pA- + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 NHMM2 cel tot + 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 NHMM2 cel tot + 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 NHMf cel tot + 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 NHMf cel tot + 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 NHEK nuc pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 NHEK nuc pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 NHEK nuc pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 NHEK nuc pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 NHEK cyt pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 NHEK cyt pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 NHEK cyt pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 NHEK cel pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 NHEK cel pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 NHEK cel pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 NHEK cel pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 NHDF cel tot + 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 NHDF cel tot + 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 HWP cel tot + 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 HWP cel tot + 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 HVMF cel tot + 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 HVMF cel tot + 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 HSMM cel pA+ + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 HSMM cel pA+ + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 HSMM cel pA- + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 HSMM cel pA- + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 HSVEC cel tot + 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 HSVEC cel tot + 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 HPIEC cel tot + 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 HPIEC cel tot + 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 HPCPL cel tot + 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 HPCPL cel tot + 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 HOB cel tot + 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 HOB cel tot + 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 hMSUC cel tot + 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 hMSUC cel tot + 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 hMSBM cel tot + 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 hMSBM cel tot + 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 hMSAT cel tot + 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 hMSAT cel tot + 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 hMNPB cel tot + 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 PlusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMNC-PB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 HMEpC cel tot + 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 PlusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HMEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 HMEC cel pA+ + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 HMEC cel pA- + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 HFDPC cel tot + 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 HFDPC cel tot + 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 HCH cel tot + 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 HCH cel tot + 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 HAoEC cel tot + 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 HAoEC cel tot + 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 HAoAF cel tot + 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 HAoAF cel tot + 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 CD34 cel tot + 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 PlusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD34+ Mobilized whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 BJ cel pA+ + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 BJ cel pA+ + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 BJ cel pA- + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 BJ cel pA- + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 AG50 cel pA+ + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 AG50 cel pA+ + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 AG50 cel pA- + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 AG50 cel pA- + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 SKNSH nuc pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 SKNSH nuc pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 SKNSH cyt pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 SKNSH cyt pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 SKNSH cel pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 SKNSH cel pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 CD14 cel pA+ + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 CD14 cel pA+ + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 CD14 cel pA- + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 CD14 cel pA- + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 MCF7 nuc pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 MCF7 nuc pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 MCF7 cyt pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 MCF7 cyt pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 MCF7 cel pA+ + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 MCF7 cel pA+ + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 MCF7 cel pA- + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 MCF7 cel pA- + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 IMR90 nuc pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 IMR90 nuc pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 IMR90 cyt pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 IMR90 cyt pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 IMR90 cel tot + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 IMR90 cel tot + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 IMR90 cel pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 IMR90 cel pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 HUVEC nuc pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 HUVEC nuc pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 HUVEC nuc pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 HUVEC nuc pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 HUVEC cyt pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 HUVEC cyt pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 HUVEC cyt pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 HUVEC cel pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 HUVEC cel pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 HUVEC cel pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 HUVEC cel pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 HeG2 nuc pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 HeG2 nuc pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 HeG2 nuc pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 HeG2 nuc pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 HeG2 cyt pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 HeG2 cyt pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 HeG2 cyt pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 HeG2 cyt pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 HeG2 cel pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 HeG2 cel pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 HeG2 cel pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 HeG2 cel pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 HeS3 nuc pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 HeS3 nuc pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 HeS3 nuc pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 HeS3 nuc pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 HeS3 cyt pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 HeS3 cyt pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 HeS3 cyt pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 HeS3 cel pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 HeS3 cel pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 HeS3 cel pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 HeS3 cel pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 CD20 cel pA+ + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 CD20 cel pA+ + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 CD20 cel pA- + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 CD20 cel pA- + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 A549 nuc pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 A549 nuc pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 A549 cyt pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 A549 cyt pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 A549 cel pA+ + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 A549 cel pA+ + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 A549 cel pA- + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 A549 cel pA- + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 K562 nuc pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 K562 nuc pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 K562 nuc pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 K562 nuc pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 K562 ncpm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 K562 ncpm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 K562 nlus tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleolus total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 K562 cyt pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 K562 cyt pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 K562 cyt pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 K562 cyt pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 K562 chrm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 K562 chrm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 K562 cel pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 K562 cel pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 K562 cel pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 K562 cel pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 H1hSC nuc pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 H1hSC nuc pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 H1hSC cyt pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 H1hSC cyt pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 H1hSC cel pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 H1hSC cel pA+ + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 H1hSC cel pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 H1hSC cel pA- + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 GM78 nuc pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 GM78 nuc pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 GM78 nuc pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 GM78 nuc pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 GM78 nlus tot + 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 GM78 nlus tot + 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 GM78 cyt pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 GM78 cyt pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 GM78 cyt pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 GM78 cyt pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 GM78 cel pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 GM78 cel pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 GM78 cel pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 GM78 cel pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewMinusSig Minus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 SKRA cel pA+ - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 SKRA cel pA+ - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 SKRA cel pA- - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 SKRA cel pA- - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 SkMC cel tot - 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 SkMC cel tot - 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 NHLF cel pA+ - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 NHLF cel pA+ - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 NHLF cel pA- - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 NHLF cel pA- - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 NHMM2 cel tot - 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 NHMM2 cel tot - 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 NHMf cel tot - 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 NHMf cel tot - 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 NHEK nuc pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 NHEK nuc pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 NHEK nuc pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 NHEK nuc pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 NHEK cyt pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 NHEK cyt pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 NHEK cyt pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 NHEK cel pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 NHEK cel pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 NHEK cel pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 NHEK cel pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 NHDF cel tot - 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 NHDF cel tot - 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 HWP cel tot - 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 HWP cel tot - 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 HVMF cel tot - 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 HVMF cel tot - 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 HSMM cel pA+ - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 HSMM cel pA+ - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 HSMM cel pA- - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 HSMM cel pA- - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 HSVEC cel tot - 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 HSVEC cel tot - 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 HPIEC cel tot - 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 HPIEC cel tot - 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 HPCPL cel tot - 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 HPCPL cel tot - 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 HOB cel tot - 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 HOB cel tot - 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 hMSUC cel tot - 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 hMSUC cel tot - 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 hMSBM cel tot - 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 hMSBM cel tot - 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 hMSAT cel tot - 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 hMSAT cel tot - 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 hMNPB cel tot - 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 MinusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMNC-PB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 HMEpC cel tot - 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 MinusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HMEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 HMEC cel pA+ - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 HMEC cel pA- - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 HFDPC cel tot - 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 HFDPC cel tot - 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 HCH cel tot - 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 HCH cel tot - 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 HAoEC cel tot - 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 HAoEC cel tot - 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 HAoAF cel tot - 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 HAoAF cel tot - 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 CD34 cel tot - 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 MinusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD34+ Mobilized whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 BJ cel pA+ - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 BJ cel pA+ - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 BJ cel pA- - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 BJ cel pA- - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 AG50 cel pA+ - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 AG50 cel pA+ - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 AG50 cel pA- - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 AG50 cel pA- - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 SKNSH nuc pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 SKNSH nuc pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 SKNSH cyt pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 SKNSH cyt pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 SKNSH cel pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 SKNSH cel pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 CD14 cel pA+ - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 CD14 cel pA+ - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 CD14 cel pA- - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 CD14 cel pA- - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MCF7 nuc pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MCF7 nuc pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MCF7 cyt pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MCF7 cyt pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MCF7 cel pA+ - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MCF7 cel pA+ - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MCF7 cel pA- - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MCF7 cel pA- - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 IMR90 nuc pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 IMR90 nuc pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 IMR90 cyt pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 IMR90 cyt pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 IMR90 cel tot - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 IMR90 cel tot - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 IMR90 cel pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 IMR90 cel pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 HUVEC nuc pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 HUVEC nuc pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 HUVEC nuc pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 HUVEC nuc pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 HUVEC cyt pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 HUVEC cyt pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 HUVEC cyt pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 HUVEC cel pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 HUVEC cel pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 HUVEC cel pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 HUVEC cel pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 HeG2 nuc pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 HeG2 nuc pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 HeG2 nuc pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 HeG2 nuc pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 HeG2 cyt pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 HeG2 cyt pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 HeG2 cyt pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 HeG2 cyt pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 HeG2 cel pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 HeG2 cel pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 HeG2 cel pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 HeG2 cel pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 HeS3 nuc pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 HeS3 nuc pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 HeS3 nuc pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 HeS3 nuc pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 HeS3 cyt pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 HeS3 cyt pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 HeS3 cyt pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 HeS3 cel pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 HeS3 cel pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 HeS3 cel pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 HeS3 cel pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 CD20 cel pA+ - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 CD20 cel pA+ - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 CD20 cel pA- - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 CD20 cel pA- - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 A549 nuc pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 A549 nuc pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 A549 cyt pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 A549 cyt pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 A549 cel pA+ - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 A549 cel pA+ - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 A549 cel pA- - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 A549 cel pA- - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 K562 nuc pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 K562 nuc pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 K562 nuc pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 K562 nuc pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 K562 ncpm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 K562 ncpm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 K562 nlus tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleolus total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 K562 cyt pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 K562 cyt pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 K562 cyt pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 K562 cyt pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 K562 chrm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 K562 chrm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 K562 cel pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 K562 cel pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 K562 cel pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 K562 cel pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 H1hSC nuc pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 H1hSC nuc pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 H1hSC cyt pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 H1hSC cyt pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 H1hSC cel pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 H1hSC cel pA+ - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 H1hSC cel pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 H1hSC cel pA- - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 GM78 nuc pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 GM78 nuc pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 GM78 nuc pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 GM78 nuc pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 GM78 nlus tot - 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 GM78 nlus tot - 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 GM78 cyt pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 GM78 cyt pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 GM78 cyt pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 GM78 cyt pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 GM78 cel pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 GM78 cel pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 GM78 cel pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 GM78 cel pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewContigs Contigs Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapContigs SKRA cel pA+ C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamContigs SKRA cel pA- C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalContigs SkMC cel tot C SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalContigs Contigs Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SkMC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapContigs NHLF cel pA+ C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamContigs NHLF cel pA- C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs NHMM2 cel tot C NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs Contigs Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs NHMf cel tot C NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs Contigs Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM.f M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapContigs NHEK nuc pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamContigs NHEK nuc pA- C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapContigs NHEK cyt pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 NHEK cyt pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 NHEK cel pA+ C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 NHEK cel pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalContigs NHDF cel tot C NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalContigs Contigs Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHDF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalContigs HWP cel tot C HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalContigs Contigs Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HWP whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalContigs HVMF cel tot C HVMF RnaSeq ENCODE Jul 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalContigs Contigs villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HVMF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapContigs HSMM cel pA+ C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamContigs HSMM cel pA- C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalContigs HSVEC cel tot C HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalContigs Contigs Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSaVEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs HPIEC cel tot C HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs Contigs Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPIEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalContigs HPCPL cel tot C HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalContigs Contigs Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPC-PL whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalContigs HOB cel tot C HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalContigs Contigs Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HOB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalContigs hMSUC cel tot C hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-UC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs hMSBM cel tot C hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-BM whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalContigs hMSAT cel tot C hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-AT whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 hMNPB cel tot C hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 Contigs Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMNC-PB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalContigs HMEpC cel tot C HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalContigs Contigs Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 HMEC cel pA+ C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 HMEC cel pA- C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs HFDPC cel tot C HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs Contigs Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HFDPC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalContigs HCH cel tot C HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalContigs Contigs Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HCH whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalContigs HAoEC cel tot C HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalContigs Contigs Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalContigs HAoAF cel tot C HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalContigs Contigs Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoAF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs CD34 cel tot C CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs Contigs hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD34+ Mobilized whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapContigs BJ cel pA+ C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamContigs BJ cel pA- C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapContigs AG50 cel pA+ C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamContigs AG50 cel pA- C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapContigs SKNSH nuc pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapContigs SKNSH cyt pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapContigs SKNSH cel pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapContigs CD14 cel pA+ C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamContigs CD14 cel pA- C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs MCF7 nuc pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs MCF7 cyt pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapContigs MCF7 cel pA+ C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamContigs MCF7 cel pA- C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapContigs IMR90 nuc pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapContigs IMR90 cyt pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalContigs IMR90 cel tot C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapContigs IMR90 cel pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs HUVEC nuc pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs HUVEC nuc pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs HUVEC cyt pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 HUVEC cyt pA- C HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapContigs HUVEC cel pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamContigs HUVEC cel pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs HeG2 nuc pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs HeG2 nuc pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs HeG2 cyt pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs HeG2 cyt pA- C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapContigs HeG2 cel pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamContigs HeG2 cel pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs HeS3 nuc pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs HeS3 nuc pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs HeS3 cyt pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 HeS3 cyt pA- C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapContigs HeS3 cel pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamContigs HeS3 cel pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapContigs CD20 cel pA+ C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamContigs CD20 cel pA- C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapContigs A549 nuc pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapContigs A549 cyt pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapContigs A549 cel pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamContigs A549 cel pA- C A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapContigs K562 nuc pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamContigs K562 nuc pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs K562 ncpm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleoplasm total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapContigs K562 cyt pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamContigs K562 cyt pA- C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs K562 chrm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 chromatin total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapContigs K562 cel pA+ C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamContigs K562 cel pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 H1hSC nuc pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 H1hSC nuc pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 H1hSC cyt pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 H1hSC cyt pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapContigs H1hSC cel pA+ C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamContigs H1hSC cel pA- C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs GM78 nuc pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs GM78 nuc pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs GM78 nlus tot C GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleolus total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs GM78 cyt pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs GM78 cyt pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapContigs GM78 cel pA+ C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamContigs GM78 cel pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewAlignments Alignments Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 SKRA cel pA+ A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 SKRA cel pA+ A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 SKRA cel pA- A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 SKRA cel pA- A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 SkMC cel tot A 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 SkMC cel tot A 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 NHLF cel pA+ A 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 NHLF cel pA+ A 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 NHLF cel pA- A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 NHLF cel pA- A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 NHMM2 cel tot A 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 NHMM2 cel tot A 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 NHMf cel tot A 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 NHMf cel tot A 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 NHEK nuc pA+ A 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2011-06-08 2012-03-08 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x U wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 NHEK nuc pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 NHEK nuc pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 NHEK nuc pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 NHEK cyt pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 NHEK cyt pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 NHEK cyt pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 NHEK cel pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 NHEK cel pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 NHEK cel pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 NHEK cel pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 NHDF cel tot A 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 NHDF cel tot A 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 HWP cel tot A 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 HWP cel tot A 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 HVMF cel tot A 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 HVMF cel tot A 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 HSMM cel pA+ A 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 HSMM cel pA+ A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 HSMM cel pA- A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 HSMM cel pA- A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 HSVEC cel tot A 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 HSVEC cel tot A 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 HPIEC cel tot A 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 HPIEC cel tot A 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 HPCPL cel tot A 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 HPCPL cel tot A 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 HOB cel tot A 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 HOB cel tot A 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 hMSUC cel tot A 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 hMSUC cel tot A 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 hMSBM cel tot A 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 hMSBM cel tot A 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 hMSAT cel tot A 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 hMSAT cel tot A 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 hMNPB cel tot A 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 Alignments Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMNC-PB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 HMEpC cel tot A 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 Alignments Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HMEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 HMEC cel pA+ A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 HMEC cel pA- A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 HFDPC cel tot A 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 Align