Genomics

Dataset Information

167

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington


ABSTRACT: This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements. For each experiment (cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Raw Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks)." For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Cells were grown according to the approved ENCODE cell culture protocols. Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolating DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (36 bp reads). Uniquely mapping high-quality reads were mapped to the genome. DNaseI sensitivity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.

ORGANISM(S): Homo sapiens  

SUBMITTER: Richard Sandstrom  ENCODE DCC    

PROVIDER: E-GEOD-29692 | ArrayExpress | 2014-05-02

SECONDARY ACCESSION(S): GSE29692SRP006947

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

The accessible chromatin landscape of the human genome.

Thurman Robert E RE   Rynes Eric E   Humbert Richard R   Vierstra Jeff J   Maurano Matthew T MT   Haugen Eric E   Sheffield Nathan C NC   Stergachis Andrew B AB   Wang Hao H   Vernot Benjamin B   Garg Kavita K   John Sam S   Sandstrom Richard R   Bates Daniel D   Boatman Lisa L   Canfield Theresa K TK   Diegel Morgan M   Dunn Douglas D   Ebersol Abigail K AK   Frum Tristan T   Giste Erika E   Johnson Audra K AK   Johnson Ericka M EM   Kutyavin Tanya T   Lajoie Bryan B   Lee Bum-Kyu BK   Lee Kristen K   London Darin D   Lotakis Dimitra D   Neph Shane S   Neri Fidencio F   Nguyen Eric D ED   Qu Hongzhu H   Reynolds Alex P AP   Roach Vaughn V   Safi Alexias A   Sanchez Minerva E ME   Sanyal Amartya A   Shafer Anthony A   Simon Jeremy M JM   Song Lingyun L   Vong Shinny S   Weaver Molly M   Yan Yongqi Y   Zhang Zhancheng Z   Zhang Zhuzhu Z   Lenhard Boris B   Tewari Muneesh M   Dorschner Michael O MO   Hansen R Scott RS   Navas Patrick A PA   Stamatoyannopoulos George G   Iyer Vishwanath R VR   Lieb Jason D JD   Sunyaev Shamil R SR   Akey Joshua M JM   Sabo Peter J PJ   Kaul Rajinder R   Furey Terrence S TS   Dekker Job J   Crawford Gregory E GE   Stamatoyannopoulos John A JA  

Nature 20120901 7414


DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of n  ...[more]

Publication: 1/2

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