814c185f406c5669b5b3d5ecf5dcc505650a1a7e ccpowell Tue Jun 11 10:33:30 2019 -0700 Updating newarch.html to include ENCODE3 tfbs announcement, refs #23243 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0a05229..20751c0 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,63 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> +<a name="061319"></a> +<h2> Jun. 16, 2019 New ENCODE 3 transcription factor binding site tracks for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2> +<p> +We are pleased to announce two new ENCODE 3 transcription factor binding site tracks for human +(GRCh37/hg19, GRCh38/hg38) assemblies. These tracks show regions of transcription factor binding +derived from a large collection of ChIP-seq experiments performed by the ENCODE project between +February 2011 and November 2018. +</p> +<p> +The ENCODE TF ChIP-seq data were processed using the +<a href="https://www.encodeproject.org/chip-seq/transcription_factor/" target="_blank">ENCODE Transcription Factor ChIP-seq Processing +Pipeline</a> to generate peaks of TF binding. Peaks from 1264 experiments (1256 in hg38) representing +338 transcription factors (340 in hg38) in 130 cell types (129 in hg38) were compiled in order to +generate these two tracks. The peaks were grouped together to produce a summary display showing +occupancy regions for each factor, seen here in the TF ChIP Clusters tracks: +<a href="https://genome.ucsc.edu/s/cocopow/hg19_tf_clusters" target="_blank">hg19</a>, +<a href="https://genome.ucsc.edu/s/cocopow/hg38_tf_clusters" target="_blank">hg38</a><br> +The underlying ChIP-seq peak data are available from the ENCODE 3 TF ChIP Peaks tracks: +<a href="https://genome.ucsc.edu/s/cocopow/hg19_tf_peaks" target="_blank">hg19</a>, +<a href="https://genome.ucsc.edu/s/cocopow/hg38_tf_peaks" target="_blank">hg38</a> +</p> +<p> +Thanks to the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Consortium</a>, +the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating +and processing the TF ChIP-seq datasets used here. The ENCODE accession numbers of the constituent +datasets are available from the peak details page. Special thanks to Henry Pratt, Jill Moore, +Michael Purcaro, and Zhiping Weng, PI, at the +<a href="https://www.umassmed.edu/zlab/" target="_blank">ENCODE Data Analysis Center (ZLab at UMass Medical Center)</a> +for providing the peak datasets, metadata, and guidance developing this track. Thanks to Kate +Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and +releasing these tracks. +</p> + <a name="60619"></a> <h2>June 6, 2019 New Genome Browser: Chinese Hamster Ovary (CHO) cell line, criGriChoV2 (<em>Cricetulus griseus</em>)</h2> <p> A genome browser is now available for the <em>Chinese Hamster Ovary cell line</em> assembly released in June 2017 by the <a href="https://www.eaglegenomics.com/eagle-case-studies/horizon-case-study/" target="_blank">Eagle Genomics Ltd</a> (CHOK1S_HZDv1). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> <a href=../cgi-bin/hgTracks?db=criGriChoV2>criGriChoV2</a></li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.eaglegenomics.com/" target="_blank"> Eagle Genomics Ltd</a></li> <li><b>Assembly date:</b> June 2017</li> <li><b>Accession ID:</b> GCA_900186095.1</li> <li><b>NCBI Genome information:</b><a href="https://www.ncbi.nlm.nih.gov/genome/2791" target="_blank" > 2791</a> <em>(Cricetulus griseus)</em></li> <li><b>NCBI Assembly information:</b><a href="https://www.ncbi.nlm.nih.gov/assembly/1422381"