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Series GSE37074 Query DataSets for GSE37074
Status Public on Oct 03, 2012
Title DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
Project Mouse ENCODE
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This track is produced as part of the mouse ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in mouse tissues and 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 (tissue/cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (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
 
Overall design Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). Fresh tissues were harvested from mice and the nuclei prepared according to the tissue appropriate protocol (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse). 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 Illumina IIx (and Illumina HiSeq by early 2011) platform (36 bp reads). Uniquely mapping high-quality reads were mapped to the genome using the bowtie aligner. DNaseI sensitivity is directly reflected in raw tag density, 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 (I-max).
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
 
Contributor(s) Sandstrom R
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA63471
Submission date Apr 06, 2012
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (53)
GSM1014148 UW_DnaseSeq_TReg_adult-8wks_C57BL/6
GSM1014149 UW_DnaseSeq_THelper-Activated_adult-8wks_C57BL/6
GSM1014150 UW_DnaseSeq_ZhBTc4_E0_diffProtB_6hr_129/Ola
Relations
SRA SRP015984

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37074_RAW.tar 19.5 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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