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Track and Table Releases
| This page contains track and table release information for the following genome assemblies: 10 Latest Changes (all assemblies) Human Feb. 2009 (GRCh37/hg19) (hg19) Human Mar. 2006 (NCBI36/hg18) (hg18) Human May 2004 (NCBI35/hg17) (hg17) Human July 2003 (NCBI34/hg16) (hg16) Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) Mouse July 2007 (NCBI37/mm9) (mm9) Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) Dog May 2005 (Broad/canFam2) (canFam2) Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) For more information about the tracks and tables listed on this page, refer to the User's Guide. Last updated 05 Dec 2011. Inquiries and feedback welcome. |
10 Latest Changes (all assemblies)
Track/Table Name | Assembly | Release Date
CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB | hg19 | 01 Dec 2011
Histone Modifications by ChIP-seq by ChIP-seq from ENCODE/Caltech | mm9 | 28 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech | mm9 | 23 Nov 2011
Histone Modifications by ChIP-seq from ENCODE/University of Washington | hg19 | 17 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard | hg19 | 29 Oct 2011
ENCODE Mapability (hg19 release 3) | hg19 | 28 Oct 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 3) | hg19 | 19 Oct 2011
RNA Subcellular Localization by Paired End diTag Sequencing from GIS/ENCODE | hg19 | 17 Oct 2011
Long RNA-seq from ENCODE/Cold Spring Harbor Lab | hg19 | 17 Oct 2011
Affymetrix Exon Array from ENCODE/Duke (Release 2) | hg19 | 13 Oct 2011
Human Feb. 2009 (GRCh37/hg19) (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))
Track/Table Name | Release Date
CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB | 01 Dec 2011
Histone Modifications by ChIP-seq from ENCODE/University of Washington | 17 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard | 29 Oct 2011
ENCODE Mapability (hg19 release 3) | 28 Oct 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 3) | 19 Oct 2011
RNA Subcellular Localization by Paired End diTag Sequencing from GIS/ENCODE | 17 Oct 2011
Long RNA-seq from ENCODE/Cold Spring Harbor Lab | 17 Oct 2011
Affymetrix Exon Array from ENCODE/Duke (Release 2) | 13 Oct 2011
Chromatin Interactions by 5C from ENCODE/University of Washington | 10 Oct 2011
Histone Modifications by ChIP-seq from ENCODE/SYDH (Release 2) | 07 Oct 2011
RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany (Release 2 - fixed p & q values and scores) | 04 Oct 2011
DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha (Release 2) | 30 Sep 2011
Proteogenomics from ENCODE/Univ. North Carolina/Boise State Univ. | 29 Sep 2011
RNA-seq from ENCODE/Stanford/Yale/USC/Harvard | 08 Sep 2011
RIP-seq from ENCODE/SUNY Albany | 29 Aug 2011
Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha | 16 Aug 2011
RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany | 15 Aug 2011
Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU | 29 Jul 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB | 18 Jul 2011
Gene Annotations from ENCODE/GENCODE Version 7 | 11 Jul 2011
Chromatin State Segmentation by HMM from ENCODE/Broad | 24 Jun 2011
Affymetrix Exon Array from ENCODE/Duke | 14 Jun 2011
DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) | 10 Jun 2011
Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago | 03 Jun 2011
Integrated Regulation from ENCODE Tracks (Transcription, Layered H3K4Me1, Layered H3K4Me3, Layered H3K27Ac, DNase Clusters, Txn Factor ChIP) | 19 May 2011
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard | 19 May 2011
ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ | 18 May 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington | 04 May 2011
RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany | 28 Apr 2011
Open Chromatin by DNaseI HS from ENCODE/Duke University | 19 Apr 2011
DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 2) | 07 Apr 2011
Affymetrix Exon Array from ENCODE/University of Washington | 01 Apr 2011
RNA CAGE Subcellular Localization from ENCODE/RIKEN | 23 Mar 2011
Open Chromatin by FAIRE-seq from ENCODE/UNC | 21 Mar 2011
CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington | 17 Mar 2011
Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) | 17 Mar 2011
RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany | 14 Feb 2011
Histone Modifications by ChIP-seq from ENCODE/University of Washington | 11 Feb 2011
Histone Modifications by ChIP-seq from ENCODE/Broad Institute | 10 Feb 2011
ENCODE Caltech (Wold Lab) RNA-seq | 08 Feb 2011
ENCODE GIS DNA PET (update: added fastq files) | 12 Jan 2011
ENCODE UW DNaseI HS | 16 Dec 2010
ENCODE HAIB Methyl RRBS | 15 Dec 2010
ENCODE UW DNaseI DGF | 14 Dec 2010
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array | 03 Dec 2010
ENCODE CSHL Sm RNA-seq | 17 Nov 2010
ENCODE Genome Institute of Singapore RNA-seq | 17 Nov 2010
ENCODE Gencode Gene Annotations (V4) | 15 Sep 2010
ENCODE Genome Institute of Singapore DNA Paired-End Ditags | 08 Sep 2010
ENCODE Mapability or Uniqueness of Reference Genome | 03 Jun 2010
ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab) | 03 Jun
Human Mar. 2006 (NCBI36/hg18) (hg18, NCBI Build 36.1)
Track/Table Name | Release Date
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI - Validation data (Release 5) | 11 Oct 2011
ENCODE Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH | 24 Jun 2011
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard | 03 Jun 2011
ENCODE Common Cell CNV (Release 2): colors in Regions view subtracks updated to new standards | 08 Apr 2011
ENCODE UW DNaseI HS (Release 4): Jurkat (G1 Phase) and HIPEpic replicates have been revoked | 24 Feb 2011
ENCODE Regulation | 12 Aug 2010
ENCODE HudsonAlpha RNA-seq | 30 Jul 2010
ENCODE RNA-seq from Yale/UC-Davis/Harvard | 09 Jul 2010
ENCODE Boston Univ (Tullius Lab) ORChID Predicted DNA Cleavage Sites | 29 Jun 2010
ENCODE Broad Histone (update to Release 3) - improved display of Signal subtracks when zoomed in to a range spanning less than 16,500 base pairs. | 16 Jun 2010
ENCODE HAIB TFBS (release 2) | 11 Jun 2010
ENCODE Caltech RNA-seq (Release 2) | 10 Jun 2010
ENCODE Mapability or Uniqueness of Reference Genome (update: adding CRG Alignability data) | 03 Jun 2010
ENCODE GIS Subcellular RNA Localization by Paired End diTag Sequencing | 01 Jun 2010
ENCODE Genome Institute of Singapore RNA-seq | 26 May 2010
ENCODE Yale TFBS (release 3) | 26 May 2010
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags (Release 2) | 24 May 2010
ENCODE Duke Affy All-Exon Arrays | 24 May 2010
ENCODE Univ. Washington Digital DNase Genomic Footprinting | 17 May 2010
ENCODE Genome Institute of Singapore DNA Paired-End Ditags | 19 Apr 2010
Fixed corrupt table from ENCODE pilot project: Gencode Gene Annotations (March 2007) | 09 Apr 2010
ENCODE Open Chromatin (release 3) | 31 Mar 2010
ENCODE Histone Modifications by Broad Institute ChIP-seq (release 3) | 23 Mar 2010
ENCODE UW Affy All-Exon Arrays (release 2) | 18 Mar 2010
ENCODE Histone Modifications by Univ. Washington ChIP-seq | 11 Mar 2010
ENCODE HudsonAlpha Methyl-seq | 05 Mar 2010
ENCODE Gencode Gene Annotations (Version 3c) | 26 Feb 2010
ENCODE Cold Spring Harbor Labs Small RNA-seq | 26 Feb 2010
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI (Release 2) | 03 Feb 2010
ENCODE Broad Histone Release 2 (release 2) | 18 Dec 2009
ENCODE Caltech RNA-seq Map Algorithm | 18 Dec 2009
ENCODE Cold Spring Harbor Labs Long RNA-seq (Release 2: GM12878, K562 whole cell) | 17 Dec 2009
ENCODE Open Chromatin, Duke/UNC/UT (Release 2) | 04 Dec 2009
ENCODE RIKEN CAGE Loc: updated download files | 30 Nov 2009
ENCODE Yale TFBS (Update several subtracks; add new subtracks) | 14 Oct 2009
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array (Update: GM12878 Nucleolus Total, HepG2 Nucleus PolyA+ and PolyA-, HepG2 Nucleolus Total) | 02 Oct 2009
ENCODE NHGRI Elnitski Negative Regulatory Elements | 24 Sep 2009
ENCODE UW Affy All Exon Arrays | 15 Sep 2009
ENCODE Common Cell-Type Copy Number Variation | 11 Sep 2009
ENCODE HudsonAlpha Methyl-seq | 11 Sep 2009
ENCODE HudsonAlpha CpG Methylation by Illumina Methyl27 | 11 Sep 2009
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI | 11 Sep 2009
ENCODE HudsonAlpha CHIP-seq (Correction to labels and metadata - TAF1) | 13 Aug 2009
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags: PolyA- in K562 nucleus and cytosol, PolyA- in prostate whole cell | 13 Aug 2009
ENCODE Cold Spring Harbor Labs Long RNA-seq (K562) | 11 Aug 2009
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
ENCODE Helicos RNA-seq (K562) | 28 Jul 2009
ENCODE Mapability or Uniqueness of Reference Genome | 24 Jul 2009
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array | 06 Jul 2009
ENCODE Open Chromatin, Duke/UNC/UT | 26 Jun 2009
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags | 09 Jun 2009
ENCODE HudsonAlpha Transcription Factor Binding Sites by ChIP-seq | 05 Jun 2009
ENCODE Gencode Gene Annotations | 08 May 2009
ENCODE SUNY Albany RNA Binding Proteins by RIP-chip | 08 Apr 2009
ENCODE Histone Modifications by Broad Institute ChIP-seq (Raw Signal tracks) | 03 Apr 2009
ENCODE Histone Modifications by Broad Institute ChIP-seq | 03 Apr 2009
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard | 13 Mar 2009
ENCODE cell culture protocols | 09 Mar 2009
ENCODE portal update for production phase | 23 Jan 2009
ENCODE 36-Way TBA Alignments and Conservation | 19 Dec 2008
Affymetrix ENCODE Extension Transcription Sites & Signal | 16 Apr 2008
ENCODE NHGRI DIPs (lift from hg17) | 23 Oct 2007
Whole-Genome ENCODE LI/UCSD TAF1 Super Track | 17 Oct 2007
ENCODE data migration from hg17 | 08 Oct 2007
Human May 2004 (NCBI35/hg17) (hg17, NCBI Build 35)
Track/Table Name | Release Date
Affymetrix ENCODE Extension Transcription Sites & Signal | 16 Apr 2008
ENCODE TBA SCONE Conservation (Update) | 19 Oct 2007
ENCODE UC Davis ChIP-chip NimbleGen (E2F1, c-Myc, TAF, POLII) | 24 Jul 2007
ENCODE Yale ChIP-chip Sites - Jun07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Jun07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Jun07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sites - Apr07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Apr07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Apr07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sites - Update to Jan07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Jan07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Jan07 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sites Update to Nov06 batch | 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Nov06 batch | 13 Jul 2007
ENCODE University of Virginia DNA Replication Origins (data update) | 30 May 2007
ENCODE Duke Dnase/chip - Feb07 batch (data addition) | 21 May 2007
ENCODE Gencode RACEfrags | 18 May 2007
ENCODE Gencode Gene Annotations (March 2007) | 04 May 2007
ENCODE UCD Ng ChIP Hits (update of cMyc and E2F1 data) | 17 Apr 2007
ENCODE Yale RFBR (Regulatory Factor Binding Regions) | 21 Feb 2007
ENCODE: UCSC EvoFold (Encode predictions analyzed in Washietl, Pedersen, et al., 2007). Replaces TBA23 EvoFold data. | 13 Feb 2007
ENCODE - University of Vienna, RNA secondary structure predicted by RNAz | 16 Jan 2007
ENCODE Yale RNA (update with October 2005 freeze data) | 10 Jan 2007
ENCODE UW/Reg QCP DNaseI Sens (replaces the following three tracks: UW/Reg DNaseI HSs, UW/Reg Q/A, UW DNase GM) | 07 Dec 2006
ENCODE Duke/NHGRI DNase (New Chip method in HepG2, Hela, GM, and CD4+) | 05 Dec 2006
ENCODE UT-Austin STAGE (update to add STAT1 tags) | 29 Nov 2006
ENCODE GIS Chip-PET (P53 in HCT116, STAT1 in HeLa, c-Myc in P493) | 07 Nov 2006
ENCODE NHGRI/PSU/UCSC TBA Conserved Elements | 05 Oct 2006
ENCODE NHGRI/PSU/UCSC TBA Conservation | 05 Oct 2006
ENCODE NHGRI/PSU TBA Alignments | 05 Oct 2006
ENCODE MSA Consensus Constrained Elements | 04 Oct 2006
ENCODE UC Berkeley MAVID Alignments | 04 Oct 2006
ENCODE UC Berkeley MAVID Conservation | 04 Oct 2006
ENCODE UC Berkeley MAVID Conserved Elements | 04 Oct 2006
ENCODE Stanford MLAGAN Conserved Elements | 04 Oct 2006
ENCODE Stanford MLAGAN Conservation | 04 Oct 2006
ENCODE Stanford MLAGAN Alignments | 04 Oct 2006
ENCODE MSA Alignment Gaps | 04 Oct 2006
ENCODE MSA Alignment Agreement | 04 Oct 2006
ENCODE UNC FAIRE track (data update) | 21 Aug 2006
8 new subtracks for ENCODE Sanger ChIP-chip track | 17 Aug 2006
ENCODE University of Uppsala, Sweden ChIP-chip Na-butyrate time series | 26 Jun 2006
ENCODE UNC FAIRE Peaks (ChIPOTle) Apr. 2006 Update, new subtrack added to UNC FAIRE | 15 Jun 2006
ENCODE UW DNase/Array GM06990 | 13 Jun 2006
ENCODE Sanger ChIP (additional data in HFL-1 cell line) | 24 May 2006
ENCODE Detection of LinEage Specific Selection (DLESS) | 19 May 2006
ENCODE Yale ChIP Sites (data replaced with 5 new transcription factors). Previous track Yale ChIP Sites renamed Yale STAT1 Sites. | 13 Jan 2006
ENCODE Yale ChIP Signal (data replaced with 5 new transcription factors). Previous track Yale ChIP Signal renamed Yale STAT1 Signal. | 13 Jan 2006
ENCODE Yale ChIP pVal (data replaced with 5 new transcription factors). Previous track Yale ChIP pVal renamed Yale STAT1 pVal. | 13 Jan 2006
ENCODE EGASP Full (Correction) | 12 Jan 2006
ENCODE EGASP Partial (data correction) | 11 Jan 2006
Recomb Hotspots: ENCODE recombination hotspots and rates | 06 Jan 2006
ENCODE Uppsala Chip (University of Uppsala, Sweden ChIP-chip coordinate corrections) | 03 Jan 2006
ENCODE Yale TAR (Replace June data with new methods) | 02 Jan 2006
ENCODE UVa DNA Rep Ori (University of Virginia DNA Replication Origins, Oct 2005 Freeze) | 29 Dec 2005
ENCODE UT-Austin STAGE (Sequence Tag Analysis of Genomic Enrichment), c-Myc in HeLa cells | 28 Dec 2005
ENCODE Affy Transfrags (updated HeLa data) | 21 Dec 2005
ENCODE Affy RNA Signal (updated HeLa data) | 21 Dec 2005
ENCODE UVa DNA Rep TR50 (University of Virginia DNA Smoothed Timing at 50% Replication, Oct 2005 Freeze) | 16 Dec 2005
ENCODE UVa DNA Rep Seg (University of Virginia DNA Replication Temporal Segmentation, Oct 2005 Freeze) | 02 Dec 2005
ENCODE Sanger ChIP Hits (Peaks and Centers, Oct 2005 Freeze) | 22 Nov 2005
ENCODE Sanger ChIP (H3, H4 histones in GM, K562 and HeLa cells, Oct 2005 Freeze) | 22 Nov 2005
ENCODE UNC FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements, Oct 2005 Freeze) | 22 Nov 2005
ENCODE UCD Ng ChIP (UC Davis ChIP-chip of E2F1, Myc in HeLa, Oct 2005 Freeze) | 18 Nov 2005
ENCODE Uppsala Chip (University of Uppsala, Sweden ChIP-chip of H3ac,HNF3b,HNF4a,USF1 in HepG2 cells, Oct 2005 Freeze) | 18 Nov 2005
ENCODE Affy Strict Sites (Affymetrix ChIP-chip of 5 factors in HL60 cells, Oct 2005 Freeze) | 18 Nov 2005
ENCODE Affy Strict (Affymetrix ChIP-chip of 5 factors in HL60 cells, Oct 2005 Freeze) | 18 Nov 2005
ENCODE Affy Strict Pval (Affymetrix ChIP-chip on 5 factors, in HL60 cells, Oct 2005 Freeze) | 18 Nov 2005
ENCODE Affy RNA (RNA abundance and transfrags, Oct 2005 Freeze) | 07 Nov 2005
ENCODE UT-Austin ChIP (c-Myc and EF24 in HeLa and 20901 fibroblasts, Oct 2005 Freeze) | 07 Nov 2005
ENCODE NHGRI DnaseI-HS (MPSS and Chip methods, in CD4 and GM09660, Oct 2005 Freeze) | 07 Nov 2005
ENCODE GIS PET RNA (update Oct 2005 Freeze and new estrogen-treated MCF7) | 07 Nov 2005
ENCODE Gencode Genes (Oct 2005 Freeze) | 07 Nov 2005
ENCODE LI Ng gIF ChIP (Addition of 5 antibodies, in HeLa cells) | 27 Oct 2005
ENCODE EGASP Update (Add Fgenesh++ corrected predictions) | 14 Oct 2005
ENCODE GIS STAT1 +/- gIF HeLa | 14 Oct 2005
ENCODE UVa DNA Rep Seg, UVa DNA Rep Ori (DNA replication timing segmentation and origins) | 04 Oct 2005
ENCODE YALE MAS TAR (additional data) | 27 Sep 2005
ENCODE YALE MAS RNA (additional data from June freeze) | 27 Sep 2005
ENCODE BU Orchid | 21 Sep 2005
ENCODE NHGRI DIPs: Whole Genome Shotgun insertion/deletion polymorphisms from Jim Mullikin/SSAHA | 21 Sep 2005
ENCODE: LI Ng gIF ChIP (HeLa) | 20 Sep 2005
ENCODE: LI Ng Validation (Pol2, Taf1, H3K4me, H3ac) | 20 Sep 2005
ENCODE Sanger ChIP-chip | 20 Sep 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - Pol II, TAF1, AcH3, H3K4me, SUZ12, and H3K27me antibodies - repackage three existing tracks into one | 20 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, P-Values) | 20 Sep 2005
ENCODE: LI gIF ChIP (HeLa) | 19 Sep 2005
ENCODE HapMap Allele Frequencies | 19 Sep 2005
ENCODE: GIS P53 5FU HCT116 | 19 Sep 2005
ENENCODE: Affy Transfrags, Affy pVal {0,2,8,32}h, Affy Sites {0,2,8,32}h | 16 Sep 2005
ENCODE: Affy RNA Signal | 16 Sep 2005
ENCODE: Yale MAS array, RNA Transcript Map, Placenta, Nimblegen Protocol | 16 Sep 2005
ENCODE: Yale MAS array, RNA Transcriptionally Active Regions, Placenta, Nimblegen Protocol | 16 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Signal) | 16 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Binding Sites) | 16 Sep 2005
ENCODE: Yale TAR | 16 Sep 2005
ENCODE: Stanford Endogenous Transcript Levels in HCT116 Cells; Stanford ChIP-chip (HCT116, Jurkat, K562 cells; Sp1, Sp3 ChIP); Stanford ChIP-chip Smoothed Score; Stanford Methylation Digest: Be2C, CRL1690, HCT116, HT1080, HepG2, JEG3, Snu182, U87; Stanford Methylation Digest Smoothed Score | 16 Sep 2005
ENCODE: Stanf Promoter | 15 Sep 2005
ENCODE: BU First Exon | 15 Sep 2005
ENCODE: Yale RNA | 15 Sep 2005
ENCODE: Sanger Assoc | 15 Sep 2005
ENCODE: UC Davis ChIP-chip Nimblegen - E2F1 ab, HeLa Cells | 15 Sep 2005
ENCODE: GIS RNA PET | 15 Sep 2005
ENCODE: TBA23 EvoFold (Predictions of RNA Secondary Structure Using TBA23, ENCODE Regions only) | 15 Sep 2005
ENCODE: Known+Pred RNA (Known and Predicted RNA Transcription) | 15 Sep 2005
ENCODE: UW/Regulome DNase I Hypersensitivity Probability | 14 Sep 2005
ENCODE: Regulome DNase I Hypersensitivity | 14 Sep 2005
ENCODE: NHGRI DNaseI-HS | 14 Sep 2005
ENCODE: Riken CAGE - predicted gene start sites | 13 Sep 2005
ENCODE Gene Prediction Workshop (EGASP) Updates | 12 Sep 2005
ENCODE Regions | 15 Sep 2004
Human July 2003 (NCBI34/hg16) (hg16, NCBI Build 34)
Track/Table Name | Release Date
ENCODE EGASP Full (Correction) | 12 Jan 2006
Recomb Hotspots: ENCODE recombination hotspots and rates | 06 Jan 2006
ENCODE GIS PET RNA (update) | 07 Nov 2005
ENCODE YALE MAS TAR (additional data) | 27 Sep 2005
ENCODE YALE MAS RNA (additional data from June freeze) | 27 Sep 2005
ENCODE Consensus Unannotated Transfrags | 30 Aug 2005
ENCODE All Introns Proximal | 17 Jul 2005
ENCODE All Introns Distal | 17 Jul 2005
ENCODE All Intergenic Proximal | 17 Jul 2005
ENCODE All Intergenic Distal | 17 Jul 2005
ENCODE Introns Proximal | 17 Jul 2005
ENCODE Introns Distal | 17 Jul 2005
ENCODE Intergenic Proximal | 17 Jul 2005
ENCODE Intergenic Distal | 17 Jul 2005
TBA23 EvoFold (Predictions of RNA Secondary Structure Using TBA23, ENCODE Regions only) | 15 Jul 2005
ENCODE Stanford LAGAN Alignments | 14 Jul 2005
ENCODE: NHGRI/PSU TBA Alignments | 14 Jul 2005
Recombination in 10 ENCODE regions (cM/Mb) | 13 Jul 2005
ENCODE Stanford LAGAN Conserved Elements | 11 Jul 2005
ENCODE Stanford LAGAN Conservation | 11 Jul 2005
Gene Prediction Workshop (EGASP) for Partial ENCODE Regions | 06 Jul 2005
Gene Prediction Workshop (EGASP) All ENCODE Regions | 06 Jul 2005
ENCODE: Riken CAGE - predicted gene start sites | 06 Jul 2005
ENCODE Gene Prediction Workshop (EGASP) Updates | 05 Jul 2005
ENCODE HapMap Allele Frequencies | 05 Jul 2005
ENCODE: Sanger Assoc | 01 Jul 2005
ENCODE: Yale MAS array, RNA Transcriptionally Active Regions, Placenta, Nimblegen Protocol | 27 Jun 2005
ENCODE: Yale MAS array, RNA Transcript Map, Placenta, Nimblegen Protocol | 27 Jun 2005
ENCODE: Affy RNA Signal, Affy Transfrags, Affy pVal {0,2,8,32}h, Affy Sites {0,2,8,32}h | 17 Jun 2005
ENCODE: Yale RNA Transcriptionally Active Regions (TARs) | 17 Jun 2005
ENCODE: Yale RNA Transcript Map (Neutrophil, Placenta and NB4 cells) | 17 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, P-Values) | 15 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Binding Sites) | 15 Jun 2005
ENCODE: Boston University ORChID | 14 Jun 2005
ENCODE: UC Davis ChIP-chip Nimblegen - E2F1 ab, HeLa Cells | 14 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Signal) | 14 Jun 2005
ENCODE: Gencode Introns (Intron validation for selected Gencode Genes) | 14 Jun 2005
Gencode Genes (Manual annotations in the ENCODE regions from the Gencode project) | 14 Jun 2005
ENCODE: ChIP-PET/GIS (data update, has cluster counts) | 14 Jun 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - Pol II, TAF1, AcH3, H3K4me, SUZ12, and H3K27me antibodies - repackage three existing tracks into one | 13 Jun 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - gamma interferon experiments | 13 Jun 2005
ENCODE: GIS RNA PET | 10 Jun 2005
ENCODE: NHGRI DNaseI-HS (data update; now includes sites from activated as well as unactivated cells) | 10 Jun 2005
ENCODE: Sanger ChIP-chip (histones H3,H4 GM06990) | 10 Jun 2005
Affymetrix ChIP-chip (Pol2 RA-stim HL60) Signal in ENCODE Regions (changed from wig to bedGraph) | 08 Jun 2005
Affymetrix ChIP-chip (Pol2 RA-stim HL60) PValue in ENCODE Regions (changed from wig to bedGraph) | 08 Jun 2005
Stanf. Promoter in ENCODE regions (data update; changed to composite track - old name: Promoter/Stanford) | 06 Jun 2005
DNA Rep/UVA in ENCODE regions (reloaded with new data) | 03 Jun 2005
ChIP-PET/GIS (P53 TFBS in ENCODE regions) | 24 May 2005
Promoters/BU (Boston Univ. Promoters in ENCODE regions) | 07 May 2005
ENCODE UCSD/Ludwig Chip (acetylated and methylated histone binding) | 06 May 2005
ENCODE UCSD Ludwig RNAP, ENCODE UCSD Ludwig TAF1 (tracks combined into composite format) | 29 Apr 2005
ChIp/Sanger (Lysine 4 methylation of histone in ENCODE regions) | 07 Apr 2005
RNA/Affy Sites (Affymetrix PolyA+ RNA from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) | 31 Jan 2005
RNA/Affy Signal (Affymetrix PolyA+ RNA abundance from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) | 31 Jan 2005
ChIP Affy Pol2 Sites (Affymetrix ChIP-chip of Pol2 from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) | 31 Jan 2005
ChIP Affy Pol2 Pval (Affymetrix ChIP-chip enrichment of Pol2 from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) | 31 Jan 2005
ChIP-chip data in ENCODE regions | 05 Nov 2004
DNA Rep/UVA (ENCODE DNA Replication data from Dutta Lab, University of VIrginia) | 03 Nov 2004
Promoter/Stanford (Promoters in ENCODE regions, from Myers lab at Stanford) | 02 Nov 2004
DNaseI-HS/NHGRI (ENCODE DNaseI Hypersensitive sites, from Collins lab, NHGRI) | 01 Nov 2004
Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2, Washington University Build 2 Version 1)
Track/Table Name | Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2, Venter Inst./Baylor/WashU Merged assembly Jan 2006 v1 edit4)
Track/Table Name | Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
Mouse July 2007 (NCBI37/mm9) (mm9, NCBI Build 37)
Track/Table Name | Release Date
Histone Modifications by ChIP-seq by ChIP-seq from ENCODE/Caltech | 28 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech | 23 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 2) | 19 Sep 2011
RNA-seq from ENCODE/LICR | 04 Aug 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR | 22 Jul 2011
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale | 22 Jul 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington | 01 Jul 2011
Histone Modifications by ChIP-seq from ENCODE/LICR | 24 Jun 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale | 07 Feb 2011
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
Rat Nov. 2004 (Baylor 3.4/rn4) (rn4, Baylor HGSC v. 3.4)
Track/Table Name | Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
Dog May 2005 (Broad/canFam2) (canFam2, Broad Institute v. 2.0)
Track/Table Name | Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009
Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4, Baylor Release 4.0)
Track/Table Name | Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters | 30 Jul 2009