6e3693e403c2c4ac5f6ed33641b900e023a4cea6 lrnassar Mon Nov 4 13:49:32 2019 -0800 Preparing to release mm10 refs #24296 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d4f6c95..2a390d0 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,31 +38,51 @@ </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="110519"></a> +<h2>Nov. 5, 2019 Expanded CRISPR track released for mouse (GRCm38/mm10)</h2> +<p> +We are pleased to announce the release of an expanded + <a href="../cgi-bin/hgTracks?db=mm10&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr1:11186551-11186838" target="_blank">CRISPR Targets track</a> for the mouse (GRCm38/mm10) +assembly. This track shows the DNA sequences targetable by CRISPR RNA guides +using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire mouse genome. CRISPR target +sites were annotated with predicted specificity (off-target effects) and predicted efficiency +(on-target cleavage) by various algorithms through the tool +<a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. The target sequence of the guide +is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. +</p> +<p class="text-center"> + <img class='text-center' src="../images/mm10CrisprAll.png" width='800' alt="CrisprAllTargets track"> +</p> + +<p> +We would like to thank Maximilian Haeussler, Hiram Clawson, and Lou Nassar for their effort +creating and releasing this data track.</p> + <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> @@ -71,31 +91,31 @@ 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>