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Series GSE36030 Query DataSets for GSE36030
Status Public on Apr 11, 2012
Title Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale
Project Mouse ENCODE
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Philip Cayting mailto:pcayting@stanford.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding, as identified by the PeakSeq algorithm (Peaks).
The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.

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). For details on the chromatin immunoprecipitation protocol used, see Euskirchen et. al., (2007), Rozowsky et. al. (2009) and Auerbach et. al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. Reads were pooled from all submitted replicates to generate the Peak and Signal files. Per-replicate aligments and sequences are available for download at downloads page (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/).
For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.01 when comparing the number of peaks above said threshold to the number of peaks obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value = 0.01 are considered to be significantly enriched compared to the input DNA control.
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhTfbs
 
Contributor(s) Snyder M, Weissman S, Cayting P
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA63475
Submission date Feb 23, 2012
Last update date Nov 20, 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 (2)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (85)
GSM912891 Stanford_ChipSeq_CH12_Pol2_IgG-mus
GSM912892 Stanford_ChipSeq_MEL_USF2_IgG-mus
GSM912893 Stanford_ChipSeq_MEL_p300_(SC-584)_IgG-rab
Relations
SRA SRP012156

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
GSE36030_RAW.tar 22.6 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
GSE36030_run_info_with_UCSC_objects.txt.gz 994 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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