how to search for ChIP_seq info

[Chen, Brenden]

Dear UCSC genome project,

I am interested in getting the coordinates of ALL Txn factors ChIP_seq data and have a technical issue that I hope you could help me with.

Using the genome table browser, I've been able to get the coordinates of all Txn factors ChIP_seq in the region(s) of interest (Thank you!). However, I was not able to find out much information concerning whether the data is a composite of Txn factor ChIP_seq from ALL cell lines (3 tiers) or from a selected few cell lines (which ones?).

I also tried a different attempt using the Search page of Downloadable ENCODE Files and chose specific cell lines and experiment type as criteria. Unfortunately, the output seemed to be raw data deposited by individual investigators and the data did not allow users to select for chromosome region(s) of interest to further refine the result.

Searching the mailing archives did not yield much success either (perhaps not with the right keywords). Thus,

Q1. is there a way to retrieve the Txn factor ChIP_seq info based on chr regions of interests AND cell lines of interests?
Q2. if currently there is no way to retrieve such kind of data in one go, what would be the alternative approaches to obtain pieces of info separately (would be laborious as currently there are 100+ txn factors used in ENCODE)?

Any help will be greatly appreciated. Thank you.

Regards,
Brenden

[Kate Rosenbloom]

Hello Brenden,

The Txn Factor ChIP-seq browser track contains clusters of enriched
sites from ChIP-seq performed in cell types from
all 3 tiers of ENCODE. You can see the complete list of cell types
included in this track on the track description page:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV2

The table you pulled from the Table Browser includes information for
each cluster indicating which cell types contributed to the cluster, and
what the signal strength for that cell type was in the peak contributing
to the cluster, but not the specific coordinates for the peaks on a
cell-specific basis. For that, you would need the individual
per-cell-type datasets. The uniform ChIP-seq peaks that were used to
generate this version of the Txn Factor ChIP track are available at the
ENCODE Analysis Track Hub, for downloads, and access with the Table
Browser (and Genome Browser). For a limited number of datasets, you can
readily extract the peak coordinates for your region of interest using
the Table Browser after loading the track hub. You can do this directly
from the browser Track Connect page, or indirectly from the ENCODE
downloads page (click the TFBS link in the Uniform Peaks section
header): http://encodeproject.org/ENCODE/downloads.html

Unfortunately the ENCODE data is so voluminous that often downloading
the files and processing at your site is necessary to extract data for
your specific needs. To extract all ChIP-seq peaks in your region of
interest from the 400+ datasets represented here, you would need to
download the TFBS Peaks (SPP) via the download link, and filter the
resulting narrowPeak BED files for your regions of interest.
Fortunately the Peak files are the most compact of the ENCODE files, so
should be relatively easy to download.

Note that the datasets represented here are based on data submitted for
the ENCODE January 2011 data freeze, with analysis reported by the
ENCODE Analysis Working Group in coordinated publications in September
2012: http://encodeproject.org/ENCODE/analysis.html.

Cheers,
Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics

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