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13 March 2009 - ENCODE Data Release: Transcription Factor Binding Sites from Yale/UC-Davis/Harvard
We are pleased to announce the release to the ENCODE DCC/UCSC public server
of the
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
(Yale TFBS, in the Regulation group).
This track shows probable binding sites of 12 transcription factors
and RNA polymerase II in 7 cell types, as determined by chromatin
immunoprecipitation followed by high-throughput sequencing.
The Genome Browser displays discrete Peaks
of enrichment and Signal graphs of enrichment density for these
experiments.
The sequence reads, quality scores, and sequence alignment coordinates from
these experiments are available for
download.
We would like to acknowledge the efforts of the Yale/UC-Davis/Harvard
ENCODE group and the work of the UCSC data wrangler for this group,
Tim Dreszer, for completing this track. We also thank
the entire UCSC ENCODE team and the UCSC Quality Assurance
group for contributing to this first ENCODE track release.
27 Feb 2009 - ENCODE February 2009 data freeze
The February 2009 ENCODE data freeze supplements the data contributed for the
November 2008 freeze, and will be used together with the earlier freeze
for the initial analysis effort of the ENCODE Consortium. Data from
this freeze is being incorporated into tracks created from the first
data freeze, and is being reviewed by the UCSC Quality Assurance team.
9 Dec. 2008 - First ENCODE whole-genome data freeze completed
The ENCODE Consortium has just completed the first freeze
(November 2008) of whole-genome experimental data
produced for the ENCODE production phase. Data submitted
to the DCC for this freeze include:
- transcription factor binding sites
- histone modifications
- DNaseI hypersensitive sites
- DNA methylation
- transcription maps and tags, localized to subcellular
compartments
- GENCODE gene annotations
Experiments during this freeze focused on the ENCODE
Tier1 cell lines -- K562 leukemia, and GM12878 lymphoblastoid
(which is also a
1000 Genomes project
sample designated for in-depth analysis of genetic variation).
The freeze also includes data
from some ENCODE Tier2 and Tier3 cell lines (see
Cell Types). The majority
of these experiments were assayed by high-throughput
sequencing (ChIP-seq, DNase-seq, and RNA-seq).
The UCSC quality team is currently reviewing these data.
When the review is complete, the browser tracks and
associated downloads will be released to the UCSC public
Genome Browser.
Thanks to the many labs who contributed data for the
initial phase of this project. We'd also like to acknowledge
the UCSC ENCODE team for data wrangling during the freeze,
and for the development and maintenance of
the ENCODE automated data submission pipeline and
associated tools: Kate Rosenbloom, Tim Dreszer, Larry Meyer,
Michael Pheasant, Ting Wang, Galt Barber, and Andy Pohl.
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