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 Released Data
 

This page lists releases of ENCODE data submitted to the UCSC Genome Browser for data storage and display during the pilot phase of ENCODE (2003 - 2007). Most of these datasets were restricted to the defined ENCODE regions.

Data Date Cell Lines
Affy EC RNA (chr21 and chr22) 16 Apr 2008 16 cell lines
Harvard SCONE Cons (update) 19 Oct 2007  
BU Orchid (update) 12 Oct 2007  
ENCODE hg18 Data Migration and Browser 8 Oct 2007  
GIS RNA and ChIP-PET (3 new datasets) 28 Sept 2007 ES cells
UC Davis ChIP-chip - Mar07 Batch 24 July 2007 HeLa, GM06990
Yale ChIP-chip - Jun07 Batch 13 Jul 2007 HeLa
Yale ChIP-chip - Apr07 Batch 13 Jul 2007 HeLa
Yale ChIP-chip - Jan07 Batch 13 Jul 2007 HeLa, K562
Yale ChIP-chip - Nov06 Batch 13 Jul 2007 HeLa, GM06990
Univ. Virginia - Replication Origins (new methods) 30 May 2007 HeLa, GM06990
Duke DnaseI HS Feb07 Batch 21 May 2007 IMR90, K562, H9
Gencode Genes Mar07 Batch, Gencode RACEfrags 18 May 2007  
Gencode RACE Frags 18 May 2007  
UC Davis ChIP Hits (E2F1 and c-Myc Peaks update) 17 Apr 2007 HeLa
Univ. Virginia DNA Replication Temporal Segmentation (Data correction) 17 Apr 2007 HeLa
Sanger ChIP-chip (update, CTCF and 4 histone mods) 21 Feb 2007 GM06990
Yale ChIP-chip RFBR 21 Feb 2007  
University of Vienna RNA secondary structure predicted by RNAz 13 Feb 2007  
UW/Regulome QCP Dnase HS (update and new cell lines) 7 Dec 2006 HeLa, GM06990, CD4, K562, HepG2 and 11 others
Duke/NHGRI DNaseI HS (New Chip method) 5 Dec 2006 CD4, GM06990, HeLaS3, HepG2
UT-Austin STAGE (STAT1) 29 Nov 2006 HeLa S3
Genome Inst. Singapore ChIP/PET (cMyc) 7 Nov 2006 P493 B cells
TBA Alignments, Conservation, Elements 5 Oct 2006  
MLAGAN Alignments, Conservation, Elements 5 Oct 2006  
MAVID Alignments, Conservation, Elements 5 Oct 2006  
UCB Alignment Agreement 5 Oct 2006  
Conserved Elements (Sep05 MSA freeze) 5 Oct 2006  
U North Carolina FAIRE (correction of Peaks data) 21 Aug 2006 2091 fibroblasts
Sanger Chip/Chip in MOLT4 and PTR8 cells 18 Aug 2006 HLF-1
University of Uppsala Chip/chip (H3Ac, H4Ac, butyrate treatment) 26 June 2006 HepG2
U North Carolina FAIRE (update of Peaks data) 15 June 2006 2091 fibroblasts
UW/Regulome Dnase/Array 13 June 2006 GM06990
Sanger Chip/Chip in HLF-1 cells 24 May 2006 HLF-1
DLESS (Detection of LinEage Specific Selection) 19 May 2006  
Yale ChIP-chip (5 new TFs) 13 Jan 2006 HeLa
Yale RNA (update) 2 Jan 2006  
University of Uppsala Chip/chip (data correction) 3 Jan 2006  
UT-Austin STAGE 28 Dec 2005 HeLa
U Virginia DNA Replication Timing and Predicted Origins 29 Dec 2004 HeLa
Affy RNA and Transfrags (HeLa update) 21 Dec 2005 HeLa
Sanger ChIP-chip (5 histone mods) 22 Nov 2005 HeLa, GM06990, K562
U North Carolina FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements 18 Nov 2005 2091 fibroblasts
UC Davis ChIP-chip (Pol2, Myc) 19 Nov 2005 HeLa
Affy ChIP-chip (updates and 3 new TFs) 18 Nov 2005 HL-60
Affy RNA and Transfrags (update) 1 Nov 2005 HL-60, HeLa, GM06990
UT-Austin Ng ChIP-chip (E2F4, c-Myc factors) 1 Nov 2005 HeLa, 2091 fibroblasts
GIS PET RNA (update) 1 Nov 2005 MCF7 (untreated, and w/ estrogen), HCT116
Gencode Genes and Introns (update) 1 Nov 2005  
NHGRI DNaseI HS (update and new GM06990) 1 Nov 2005 CD4, GM06990
UCSD/LI Ng ChIP-chip (update and new TFs) 27 Oct 2005 HeLa
GIS ChIP/PET (STAT1) 14 Oct 2005 HeLa
Boston University ORChID (update) 21 Sept 2005
TBA23 EvoFold RNA Structure Predictions 15 July 2005
Regulome DNaseI HS and Sens 14 July 2005
Regulome Plate Q/A and Amplicons 14 July 2005
MSA Consensus Elements 14 July 2005
TBA alignments with Conservation 14 July 2005
Stanford MLAGAN Alignments and Conservation 14 July 2005
Oxford Recombination 13 July 2005
EGASP Genes Full, Partial and Update 6 July 2005
Stanford DNA Methylation 6 July 2005
Stanford ChIP-chip and RNA 6 July 2005
RIKEN FANTOM3 CAGE Tags 6 July 2005
EGASP Gene Updates 5 July 2005
HapMap SNP's 5 July 2005
NHGRI WGS Indels 1 July 2005
Sanger Association 1 July 2005
Sanger ChIP-chip update 1 July 2005
Yale RNA on Nimblegen 27 June 2005
Affymetrix ChIP-chip and RNA 17 June 2005
Yale ChIP-chip on multiple arrays 17 June 2005
Yale RNA on Affy 17 June 2005
Gencode Genes and Intron Validation 14 June 2005
UC Davis E2F1 ChIP-chip 14 June 2005
Boston University ORChID (Hydroxyl Radical Cleavage) 14 June 2005
UCSD/Ludwig Institute ChIP-chip on Nimblegen 13 June 2005
UCSD/Ludwig Institute ChIP-chip 13 June 2005
GIS RNA PET 10 June 2005
NHGRI DnaseI HS 10 June 2005
Sanger Histone Modification ChIP-chip (update) 9 June 2005
Stanford Promoters (update) 6 June 2005
University of Virginia DNA Replication Timing (update) 3 June 2005
Genome Institute of Singapore P53 TFBS ChIP/PET 24 May 2005
Boston University First Exon 23 May 2005
UCSD/Ludwig Institute Histone Modification ChIP-chip 6 May 2005
Sanger Histone Modification ChIP-chip 7 Apr 2005
Affymetrix ChIP-chip and RNA enrichment 31 Jan 2005
UCSD/Ludwig Institute ChIP-chip 5 Nov 2004
University of Virginia DNA Replication Timing 3 Nov 2004
Stanford Promoters 2 Nov 2004
NHGRI DNaseI Hypersensitive Sites 1 Nov 2004



Last updated 30 September 2008. Inquiries and feedback welcome.