0ffa51e45bcc6d728797d7fb004c95b4387baef7 gperez2 Tue Apr 11 09:42:09 2023 -0700 Announcing the release of the cross tissue nuclei track for hg38, refs #29954 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9edee73..bab4865 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,70 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> +<a name="041023"></a> +<h2>Apr. 10, 2023 New Cross Tissue Nuclei track for hg38</h2> +<p> +We are happy to announce the release of the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=crossTissueMaps" target="_blank" +>Single-Nuclei Cross-Tissue Map</a> track for the human assembly +<a href="/cgi-bin/hgGateway?db=hg38" target="_blank">GRCh38/hg38</a>. This +track collection contains three bar chart tracks of RNA expression. The first track, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=crossTissueMapsTissueCellType" target="_blank" +>Cross Tissue Nuclei</a>, +allows cells to be grouped together and faceted on up to 4 categories: tissue, cell class, cell +subclass, and cell type. The second track, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=crossTissueMapsFullDetails" target="_blank" +>Cross Tissue Details</a>, +allows cells to be grouped together and faceted on up to 7 categories: tissue, cell class, cell +subclass, cell type, granular cell type, sex, and donor. The third track, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gtexImmuneAtlasFullDetails" target="_blank" +>GTEx Immune Atlas</a>, +allows cells to be grouped together and faceted on up to 5 categories: tissue, cell type, cell +class, sex, and donor. +<p> +This track collection shows data from +<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9383269/" target="_blank"> +Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function</a>. +The dataset dataset covers ~200,000 single nuclei from a total of 16 human donors across 25 samples, +using 4 different sample preparation protocols followed by droplet based single-cell RNA-seq. The +samples were obtained from frozen tissue as part of the +<a href="https://commonfund.nih.gov/GTEx/index" target="_blank"> +Genotype-Tissue Expression (GTEx) project</a>. Samples were taken from the esophagus, skeletal +muscle, heart, lung, prostate, breast, and skin. The dataset includes 43 broad cell classes, some +specific to certain tissues and some shared across all tissue types. Please see the +<a href="https://gtexportal.org/home/singleCellOverviewPage" target="_blank">GTEx portal</a> +for further interactive displays and additional data.</p> +<p> +We would like to thank the GTEx investigators, analysts, and portal team for providing this data. +We would also like to thank Jim Kent, Brittney Wick, Chris Lee, and Gerardo Perez for integrating +the data into the UCSC Genome Browser. +</p> + + <a name="032923"></a> <h2>Mar. 29, 2023 Updated DGV tracks for hg19/hg38</h2> <p> We are pleased to announce an update to the DGV tracks for the <a href="/cgi-bin/hgTrackUi?db=hg38&g=dgvPlus" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&g=dgvPlus" target="_blank">hg19</a> human assemblies. The tracks display copy number variants (CNVs), insertions/deletions (InDels), inversions and inversion breakpoints annotated by the <a href="http://dgv.tcag.ca/dgv/app/home" target="_blank">Database of Genomic Variants</a> (DGV), which contains genomic variations observed in healthy individuals. For the hg38 update, the Structural Variant Regions track now has 825,343 total variants and the Supporting Structural Variants track now has 7,270,185 total variants. For the hg19 update, Structural Variant Regions track now has 826,661 total variants and the Supporting Structural Variants track now has 7,346,512 total variants. More information on these tracks can be found on the <a href="/cgi-bin/hgTrackUi?db=hg38&g=dgvPlus#TRACK_HTML" target="_blank">track description page</a>.