2693ceee58c1848dbe7f051f5107a6e60406dc62 ccpowell Thu Oct 31 16:04:27 2019 -0700 Updating release docs for ENCODE 3 Reg. supertrack, refs #23880 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index aec471d..bbd043e 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,64 @@ </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="110119"></a> +<h2>Nov. 1, 2019 New ENCODE 3 Regulation super-track set available on mouse (GRCm38/mm10) assembly</h2> +<p> +We are pleased to announce the new <a target="_blank" +href="../cgi-bin/hgTrackUi?db=mm10&g=encode3Reg">ENCODE 3 Regulation super-track</a> +for the mouse (GRCm38/mm10) assembly. The <a target="_blank" href="https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements">ENCODE project</a> +has established an epigenomic resource for mammalian development, profiling a diverse panel of +mouse tissues at eight developmental stages from 10.5 days post conception until birth. The ENCODE +3 Regulation super-track is composed of the three following composite tracks: +<ul> + <li> <a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=encode3RenChromHmm">Chromatin State</a> - + presents chromatin state annotations derived from ChIP-seq of histone modifications.</li> + <li> <a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=encode3RenHistone">Histone Modifications</a> - + presents the results of a comprehensive study of chromatin state across these developmental + stages, based on 1,128 ChiP-seq assays of 8 histone modifications in 12 tissues.</li> + <li> <a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=encode3RenAtac">Open Chromatin</a> - + presents the results of a comprehensive study of chromatin accessibility across these + developmental stages, based on 122 ATAC-seq assays in 12 tissues.</li> +</ul></p> +<p class="text-center"> + <img class='text-center' src="../images/enR.png" width='700' alt="Example of the ENCODE 3 Regulation supertrack"> +</p> + +<p> +Thanks to David Gorkin and Yanxiao Zhang at the <a target="_blank" +href="http://renlab.sdsc.edu/renlab_website//">Ren lab (UCSD/Ludwig Institute for Cancer Research)</a> +and Iros Barozzi of the <a target="_blank" +href="https://biosciences.lbl.gov/divisions/egsb/">Environmental Genomics and Systems Biology Division</a> +at the Lawrence Berkeley National Laboratory for providing this data and assisting with track +development at UCSC. We would also like to thank Kate Rosenbloom, Conner Powell and the UCSC Genome +Browser team for their efforts on this release. +</p> + + <a name="102819"></a> <h2>Oct. 28, 2019 gnomAD data now available on human (GRCh38/hg38) assembly</h2> <p> We are pleased to announce the new <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&c=chr22&g=gnomadVariants">gnomAD Variants super-track</a> for the Human (GRCh38/hg38) assembly. This super-track currently includes <strong>gnomAD v3</strong> and <strong>gnomAD v2</strong>.</p> <p> <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&c=chr22&g=gnomadGenomesVariantsV3"><strong>gnomAD v3</strong></a> contains variants from 71,702 whole genomes (and no exomes), all mapped to the GRCh38/hg38 reference sequence. For more information on gnomAD v3, see the following <a target="_blank" href="https://macarthurlab.org/2019/10/16/gnomad-v3-0/">blog post</a>.</p> <p> <a target="_blank"