ff44777ccc8784341c946036e870b540dfefedd8 gperez2 Mon Aug 2 17:27:01 2021 -0700 Adding new assembly xenTro10 to newsarch page, refs #24693 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index a6494ba..bad4074 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,74 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <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> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="080221"></a> +<h2>Aug. 02, 2021 New Genome Browser: X. tropicalis, xenTro10 (<em>Xenopus tropicalis</em>)</h2> +<p> +A genome browser is now available for the <em>Xenopus tropicalis</em> assembly released in Nov. 2019 by the +<a href="https://www.berkeley.edu/" target="_blank"> University of California, Berkeley</a> (UCB_Xtro_10.0). +<h3>About the assembly:</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=xenTro10" + target="_blank">xenTro10</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.berkeley.edu/"> +University of California, Berkeley</a></li> + <li><b>Assembly date:</b> Nov. 2019</li> + <li><B>Accession ID:</B> GCF_000004195.4</li> + <li><B>NCBI Genome ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/genome/80' +TARGET='_blank'>80</A> (<em>Xenopus tropicalis</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/assembly/5323661' +TARGET='_blank'>5323661</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/577946' +TARGET='_blank'>577946</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN13041969' +TARGET='_blank'>SAMN16261960</A></li> + <li><b>Scaffold count: </b>167</li> + <li><b>Total size: </b>1,451,301,209</li> + <li><a href="../goldenPath/credits.html#xentro_credits" +target="_blank" >Acknowledgments</a></li> +</ul> +<h3>Data and Downloads:</h3> +<ul> + <li><a href="../goldenPath/credits.html#xentro_use" +target="_blank" >Data use conditions and restrictions</a></li> + <li><a href="../goldenPath/help/ftp.html" +target="_blank" >Rsync</a> and +<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/" +target="_blank" >FTP</a></li> + <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro" +target="_blank" >Downloads page</a></li> +</ul> +</p> +<p> +We would like to thank the University of California, Berkeley for creating this new X. tropicalis assembly. +We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for the development and release of +the xenTro10 genome browser. +</p> + <a name="072021"></a> <h2>July 20, 2021 Updated GENCODE tracks released for hg38, hg19, and mm39</h2> <p> We have updated our GENCODE gene datasets to the latest releases; v38 for human (hg38 & hg19) and v27 for the mouse genome assembly (mm39). These new annotation data were released by GENCODE in May 2021 and correspond to the Ensembl Genes 104 dataset. </p> <p> These tracks can be found in our All GENCODE super-track folder, with subset tracks and abundant filter options. This super-track contains many previous versions of the GENCODE genes for easy comparison. From the <a href="https://www.gencodegenes.org/human/stats.html"> GENCODE stats page</a>,