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).
The sequence reads, quality scores, and alignment coordinates from
these experiments are available for download.
Display Conventions and Configuration
This track is a multi-view composite track that contains multiple data types
(views). For each view, there are multiple subtracks that
display individually on the browser. Instructions for configuring multi-view
tracks are here.
ENCODE tracks typically contain one or more of the following views:
- Peaks
- Regions of signal enrichment based on processed data
(usually normalized data from pooled replicates). ENCODE Peaks tables contain
fields for statistical significance, including FDR
(qValue).
- Signal
- Density graph (wiggle) of signal enrichment based on
processed data.
Methods
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.
Expression data generated as confirmation of the TFBS data
can be found in the
Yale Poly-A tracks (coming soon).
Release Notes
Update to Release 4 (Feb 2012): the GM12878/NFKB (IgG-rab) experiments and files have been revoked
because the incorrect raw data files were used for generation of the processed data.
This is Release 4 (June 2011) of this track, which includes 2 additional
experiments and 2 experiments, K562/NF-YA and K562/NF-YB that were present
in earlier releases have been removed.
A number of previously released datasets have been replaced by updated versions.
The affected database tables and files include 'V3'
in the name, and metadata is marked with "submittedDataVersion=V3",
followed by the specific reason. The specific reason is:
Includes previously missing sequence data.
Previous versions of files are available for download from the
FTP site
Credits
These data were generated and analyzed by the labs of
Michael Snyder,
Mark Gerstein and
Sherman Weissman at Yale University;
Peggy Farnham at UC Davis; and
Kevin Struhl at Harvard.
Contact: the Gerstein lab.
References
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M et al.
CREB binds to multiple loci on human chromosome 22.
Mol Cell Biol. 2004 May;24(9):3804-14.
Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al.
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
Genome Res. 2007 Jun;17(6):898-909.
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M et al.
Distribution of NF-kappaB-binding sites across human chromosome 22.
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al.
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Nat Methods. 2007 Aug;4(8):651-7.
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Nat Biotechnol. 2009 Jan;27(1):66-75.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column on the track configuration page and
the download page. The full data release policy for ENCODE is available
here.
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