e336d663540641bf7e423e9398035a4a612b144f Merge parents a802e81 8260118 jnavarr5 Thu Oct 31 16:43:13 2019 -0700 Fixing a merge conflict. Commenting out Connor's announcement until tomorrow. Announcing the LRG update for hg19 and hg38, refs #24285 diff --cc src/hg/htdocs/goldenPath/newsarch.html index 6936b92,bbd043e..d4f6c95 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@@ -38,45 -38,64 +38,78 @@@ </ul> </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="103119"></a> +<h2>Oct. 31, 2019 Locus Reference Genomic (LRG) update for human</h2> +<p> +We are pleased to announce an update to the Locus Reference Genomic (LRG) regions track for human, +(<a href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=lrg" target="_blank">GRCh37/hg19</a>) and +<a href="../../cgi-vin/hgTracksUi?db=hg38&c=chrX&g=lrg" target="_blank">(GRCh38/hg38)</a>. Each LRG +record also includes at least one stable transcript on which variants may be reported. These +transcripts appear in the LRG Transcripts track in the Gene and Gene Predictions track section.</p> +<p> +This track was produced at UCSC using <a href="ftp://ftp.ebi.ac.uk/pub/databases/lrgex/" +target="_blank">LRG XML files</a>. Thanks to +<a href="http://www.lrg-sequence.org/documentation/lrg-collaborators/" +target="_blank">LRG collaborators</a> for making these data available. We would also like to thank +Angie Hinrichs and Jairo Navarro for creating and releasing these tracks.</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>