NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE31477 Query DataSets for GSE31477
Status Public on Aug 30, 2011
Title ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/Harvard
Project ENCODE
Organism Homo sapiens
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:[email protected]). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:[email protected]).

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). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. 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 (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. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et al. (2007) and Rozowsky 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.
For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate <= 0.05 when comparing the number of peaks above threshold as compared the number 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 <= 0.05 are considered to be significantly enriched compared to the input DNA control.
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs
 
Contributor(s) Snyder M, Gerstein M, Weissman S, Farnham P, Struhl K
Citation(s) 22955616
BioProject PRJNA63447
Submission date Aug 18, 2011
Last update date Nov 10, 2021
Contact name ENCODE DCC
E-mail(s) [email protected]
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (3)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (426)
GSM782122 USC_ChipSeq_HepG2_TCF7L2_UCDavis
GSM782123 USC_ChipSeq_HCT-116_TCF7L2_UCDavis
GSM782124 USC_ChipSeq_HEK293_TCF7L2_UCDavis
Relations
SRA SRP007993

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
GSE31477_RAW.tar 146.9 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
GSE31477_run_info_with_UCSC_objects.txt.gz 9.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap