f279f92f74cafe040582a1bc8fe935e947f636a9 gperez2 Fri Mar 13 18:23:40 2026 -0700 Announcing the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19, refs #36826 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9b8b4f21925..33516507892 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,75 @@ <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 found <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 our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2026"></a> +<a name="031626"></a> +<h2>Mar. 16, 2026 New DNA Methylation track: Human Methylation Atlas Summary and Signals tracks</h2> +<p> +We are excited to announce the release of the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=humanMethylationAtlasSummary&position=default" target="_blank" +>Human Methylation Atlas Summary</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=humanMethylationAtlasSignals&position=default" +target="_blank">Signals</a> tracks for hg38 and hg19, available in the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=dnaMethylation&position=default" target="_blank" +>DNA Methylation superTrack</a>. The Human Methylation Atlas tracks display genome-wide DNA +methylation profiles from deep whole-genome bisulfite sequencing (WGBS) of 39 primary human cell +types sorted from 205 healthy tissue samples. +</p> +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/QAtester/humanMethylationAtlas" target="_blank"> + <img src="../images/newsArchImages/humanMethylationAtlas.png" alt="Example of cell-type specific + unmethylated regions and methylation signals (hg38, chr2:3,233,601-3,284,760) for blood, + neuronal, pancreatic, and thyroid cell types" width='60%'></a> +</div> +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=humanMethylationAtlasSummary&position=default" +target="_blank">Human Methylation Atlas Summary track</a> consists of three subtracks: +</p> +<ul> + <li><b>All Unmethylated Regions</b> - unmethylated genomic regions for each of the 39 cell + types.</li> + <li><b>Putative Enhancers from Unmethylated Regions</b> - putative enhancers derived from + unmethylated regions for 32 of the 39 cell types. + </li> + <li><b>Top 250 Unmethylated Regions per Cell Type</b> - the top 250 most specifically unmethylated + regions in each of the 39 cell types. + </li> +</ul> +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=humanMethylationAtlasSignals&position=default" +target="_blank">Human Methylation Atlas Signals track</a> displays per-cell-type methylation beta +values (0-1 scale) across the genome, with <b>merged</b> tracks combining all replicates per cell +type and <b>replicate</b> tracks for each individual sample. +</p> +<p> +We would like to thank the Dor, Kaplan, and Glaser laboratories at the Hebrew University +of Jerusalem and collaborating institutions for generating and providing these data. +</p> + + <a name="031326"></a> <h2>Mar. 13, 2026 gnomAD v4 Exome and v3 Genome coverage tracks for hg38</h2> <p> We are pleased to announce the release of two new coverage tracks from the <a href="https://gnomad.broadinstitute.org/" target="_blank">Genome Aggregation Database (gnomAD)</a> on the human GRCh38/hg38 assembly. These tracks are part of the <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">Genome Aggregation Database (gnomAD)</a> track collection. </p> <p> The <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad4ExomeCoverage">gnomAD v4 Exome Coverage</a> track displays per-base sequencing coverage statistics derived from the gnomAD v4.0 exome callset. Coverage was computed across all gnomAD v4 exome samples using gVCFs produced with a 3-bin blocking scheme based on reference genotype quality