ENC DNase/FAIRE Uniform DNaseI HS Track Settings
 
DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis

Track collection:
ENCODE Open Chromatin by DNaseI HS and FAIRE

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 1  GM12878  GM12878 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 1  H1-hESC  H1-hESC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 1  K562  K562 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2  HUVEC  HUVEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2  HeLa-S3  HeLa-S3 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2  HepG2  HepG2 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2*  A549  A549 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2*  B cells CD20+  CD20+ B cell DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2*  MCF-7  MCF-7 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 2*  Monocytes CD14+  Monocytes-CD14+ DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AG04449  AG04449 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AG04450  AG04450 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AG09309  AG09309 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AG09319  AG09319 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AG10803  AG10803 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AoAF  AoAF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  AoSMC  AoSMC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  BE2 C  BE2_C DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  BJ  BJ DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  CD34+ Mobilized  CD34+_Mobilized DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  CLL  CLL DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  CMK  CMK DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Caco-2  Caco-2 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Chorion  Chorion DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  FibroP  FibroP DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Fibrobl  Fibrobl DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM06990  GM06990 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM12864  GM12864 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM12865  GM12865 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM12891  GM12891 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM12892  GM12892 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM18507  GM18507 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM19238  GM19238 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM19239  GM19239 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  GM19240  GM19240 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Gliobla  Gliobla DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  H7-hESC  H7-hESC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  H9ES  H9ES DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HA-h  HA-h DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HA-sp  HA-sp DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HAEpiC  HAEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HAc  HAc DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HBMEC  HBMEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HCF  HCF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HCFaa  HCFaa DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HCM  HCM DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HCPEpiC  HCPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HCT-116  HCT-116 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HConF  HConF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HEEpiC  HEEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HFF  HFF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HFF-Myc  HFF-Myc DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HGF  HGF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HIPEpiC  HIPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HL-60  HL-60 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMEC  HMEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMF  HMF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-LBl  HMVEC-LBl DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-LLy  HMVEC-LLy DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dAd  HMVEC-dAd DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dBl-Ad  HMVEC-dBl-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dBl-Neo  HMVEC-dBl-Neo DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dLy-Ad  HMVEC-dLy-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dLy-Neo  HMVEC-dLy-Neo DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HMVEC-dNeo  HMVEC-dNeo DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HNPCEpiC  HNPCEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HPAEC  HPAEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HPAF  HPAF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HPDE6-E6E7  HPDE6-E6E7 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HPF  HPF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HPdLF  HPdLF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HRCEpiC  HRCEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HRE  HRE DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HRGEC  HRGEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HRPEpiC  HRPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HSMM  HSMM DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HSMM emb  HSMM_emb DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HSMMtube  HSMMtube DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HTR8svn  HTR8svn DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HVMF  HVMF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  HeLa-S3(IFNa)  HeLa-S3 (IFNa) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Hepatocytes  Hepatocytes DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Huh-7  Huh7 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Huh-7.5  Huh7.5 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  iPS  iPS DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Ishikawa(Estr)  Ishikawa (Estradiol) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Ishikawa(Tamox)  Ishikawa (Tamoxifen) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Jurkat  Jurkat DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  LNCaP  LNCaP DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  LNCaP(Andr)  LNCaP (Androgen) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  MCF-7(Hypox)  MCF-7 (Hypoxia) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Medullo  Medullo DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Melano  Melano DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Myometr  Myometr DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NB4  NB4 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NH-A  NH-A DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NHDF-Ad  NHDF-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NHDF-neo  NHDF-neo DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NHEK  NHEK DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NHLF  NHLF DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  NT2-D1  NT2-D1 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Osteobl  Osteobl DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  PANC-1  PANC-1 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  pHTE  pHTE DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  PanIsletD  PanIsletD DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  PanIslets  PanIslets DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  PrEC  PrEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  ProgFib  ProgFib DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  RPTEC  RPTEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  RWPE1  RWPE1 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  SAEC  SAEC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  SK-N-MC  SK-N-MC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  SK-N-SH RA  SK-N-SH_RA DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  SKMC  SKMC DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Stellate  Stellate DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  T-47D  T-47D DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Th0  Th0 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Th1  Th1 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Th2  Th2 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Urothelia  Urothelia DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  Urothelia(UT189)  Urothelia (UT189) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  WERI-Rb-1  WERI-Rb-1 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  WI-38  WI-38 DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  WI-38(Tamox)  WI-38 (Tamoxifen) DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
 
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 3  8988T  8988T DNaseI HS Uniform Peaks from ENCODE/Analysis    Schema 
    
Downloads
Data version: ENCODE Jan 2011 Freeze (Sept 2012 Analysis Pubs)

Description

The ENCODE Analysis Working Group (AWG) has performed uniform processing on datasets produced by multiple data production groups in the ENCODE Consortium. This track represents a uniform set of open chromatin elements (DNaseI hypersensitive sites) in 125 ENCODE cell types, based on DNase-seq data produced by the "Open Chromatin" (Duke/UNC/UT-A) and University of Washington (UW) ENCODE groups from the project inception in 2007 through the ENCODE January 2011 data freeze. The AWG uniform datasets are used in downstream analysis pipelines by members of the ENCODE Consortium and are one of the primary sources of data referenced in the 2012 ENCODE integrative analysis paper (ENCODE Project Consortium 2012). More information about the ENCODE integrative analysis is here.

The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks:

Display Conventions and Configuration

The display for this track shows site location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. The display can be filtered to higher valued items, using the 'Minimum signal' configuration item.

This track is a composite annotation track containing multiple subtracks, one for each cell type. The display mode and filtering of each subtrack can be individually controlled. For more information about track configuration, see Configuring Multi-View Tracks.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. The UCSC Accession listed in the metadata can be used with the File Search tool to retrieve primary data files underlying datasets of interest.

In the subtrack selection list, the ENCODE tier (priority) is listed for each cell type. Tier 1 and Tier 2 represent categories with cell types designated for intensive study by the ENCODE investigators. After the January 2011 data freeze, an additional set of cell types were promoted from Tier 3 to Tier 2 to broaden the list of intensively studied cell types. These cell types are listed as Tier 2* in the subtrack list here (and are described as 'newly promoted to tier 2: not in 2011 analysis' on the ENCODE Common Cell Types page).

Methods

The DNase-seq aligned sequence reads (BAM files) from the primary data tracks listed above were processed using the UW HotSpot pipeline (as described in the UW DnaseI HS track description above). First, "hotspots" (i.e. broad, variable-sized regions of generalized chromatin accessibility) were identified using a relaxed threshold. Then more stringent "narrowPeaks" (False Discovery Rate 1% peaks) were generated by first thresholding hotspots (using random simulation) at FDR 1%, and then (essentially) locating local maxima of the tag density (150 bp window, sliding every 20 bp) within the hotspots. FDR 1% peaks were set to a fixed width of 150 bp.

The Duke DNase primary data were pre-processed to reduce variability by combining all replicates for a given cell-type and subsampling at a level of 30 million tags. For the UW data, the replicate 1 calls from the primary UW DNaseI HS data track were used. For the 14 cell types where both groups have data, a collapsed set of FDR 1% peaks were generated by taking a non-overlapping selection of the calls from both centers and giving preference to the peak with the higher z-score when calls overlapped. A collapsed set of hotspots on these cell types was generated by merging the calls from both centers (taking the union interval of overlapping intervals).

Credits

The processed data for this track were generated by the University of Washington ENCODE group on behalf of the ENCODE Analysis Working Group. Credits for the primary data underlying this track are included in track description pages listed in the Description section above.

Contact: Robert Thurman (University of Washington)

References

ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82.

See also the references in the related ENCODE Duke DNaseI HS and ENCODE UW DnaseI HS tracks.

Data Release Policy

While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available.