4738e2765fa6ddcd9025f53ddfc1da7bf8f68fb0 bwick Tue Nov 9 08:38:00 2021 -0800 Adding new section about release of scRNA-seq track group. refs #26964 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 42a6586..4aea8c1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,30 +38,238 @@ </ul> </div> <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="11XX21"></a> +<h2>Nov. XX, 2021 Releasing A New Genome Browser Track Group: Single-Cell RNA-seq</h2> +<p> +We are excited to release a new Genome Browser track group with single-cell +RNA-seq (scRNA-seq) datasets for the hg38 assembly. We are starting with 14 +scRNA-seq tracks covering different major organs of the body.</p> +<p class ="text-center"> + <img class="text-center" src="../images/newsArchImages/scRNAseq_trackgroup.jpg" width="800px"> +</p> +<p> +Each new single-cell track contains anywhere from 2-19 individual mRNA +expression tracks in <a target="_blank" +href="https://genome.ucsc.edu/goldenPath/help/barChart.html">barChart</a> +format. By default, tracks display gene expression per individual cell type +annotation and are colored according to cell class:</p> +<table cellpadding="2"> + <thead> + <tr> + <th style="border-bottom: 2px solid;">Color</th> + <th style="border-bottom: 2px solid;">Cell Classification</th> + </tr> + </thead> + <tbody> + <tr> + <td style="background-color: #f0c000; padding-left: 20px"></td> + <td>neural</td> + </tr> + <tr> + <td style="background-color: #707070; padding-left: 20px"></td> + <td>stem cell</td> + </tr> + <tr> + <td style="background-color: #ff8838; padding-left: 20px"></td> + <td>adipose</td> + </tr> + <tr> + <td style="background-color: #b05020; padding-left: 20px"></td> + <td>fibroblast</td> + </tr> + <tr> + <td style="background-color: #e02900; padding-left: 20px"></td> + <td>myeloid</td> + </tr> + </tr> + <tr> + <td style="background-color: #f01111; padding-left: 20px"></td> + <td>immune</td> + </tr> + </tr> + <tr> + <td style="background-color: #ff334a; padding-left: 20px"></td> + <td>lymphoid</td> + </tr> + </tr> + <tr> + <td style="background-color: #c000c0; padding-left: 20px"></td> + <td>muscle</td> + </tr> + </tr> + <tr> + <td style="background-color: #6000b0; padding-left: 20px"></td> + <td>hepatocyte</td> + </tr> + </tr> + <tr> + <td style="background-color: #0000ff; padding-left: 20px"></td> + <td>kidney tubule</td> + </tr> + </tr> + <tr> + <td style="background-color: #0050ff; padding-left: 20px"></td> + <td>secretory</td> + </tr> + </tr> + <tr> + <td style="background-color: #0072d6; padding-left: 20px"></td> + <td>ciliated</td> + </tr> + </tr> + <tr> + <td style="background-color: #0099c0; padding-left: 20px"></td> + <td>epithelial</td> + </tr> + </tr> + <tr> + <td style="background-color: #00c000; padding-left: 20px"></td> + <td>endothelial</td> + </tr> + </tr> + <tr> + <td style="background-color: #80d000; padding-left: 20px"></td> + <td>glia</td> + </tr> + </tbody> +</table> +<p> +When available, expression tracks organized by other categories such as sex, +donor, sample, detailed cell type, etc. are also included in these container +tracks.</p> +<p> +Clicking on any of the track titles below will lead to the track description +page, which includes additional information and allows for configuration of +various display options. <br><br>This release includes the following +tracks:<br></p> +<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?&g=bloodHao&position=default">Blood (PBMC) Hao</a> +- This track displays peripheral blood mononuclear cell expression data from +<a target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/34062119/">Hao <em>et al.</em>, 2020</a> +for 3 levels of cell type annotations, donor, phase, and time.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=colonWang&position=default">Colon Wang</a> +- This track shows colon expression data from +<a target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/31753849/">Wang <em>et al.</em>, 2020</a> +grouped by cell type and donor.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=cortexVelmeshev&position=default">Cortex Velmeshev </a> +- This track shows cortex expression data from +<a target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/31097668/">Velmeshev <em>et al.</em>, 2019</a> +grouped by cell type, sex, sample, donor, and diagnosis.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=fetalGeneAtlas&position=default">Fetal Gene Atlas</a> +- This track shows expression data from +<a target="_blank" href="">Cao <em>et al.</em>, 2020</a> +binned by cell type and other categories including sex, organ, experiment, donor, etc.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=heartCellAtlas&position=default">Heart Cell Atlas</a> +href="/cgi-bin/hgTrackUi?db=hg38&g=heartCellAtlas&position=default">Heart Cell +Atlas</a> - This track shows heart expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/32971526/">Litviňuková <em>et +al.</em>, 2020</a> binned by cell type and various categories including cell +state, sample, region, donor, age, etc.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=ileumWang&position=default">Ileum Wang</a> - +This track shows ileum expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/31753849/">Wang <em>et al.</em>, 2020</a> +grouped by cell type and donor.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=kidneyStewart&position=default">Kidney +Stewart</a> - This track shows kidney expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/31604275/">Stewart <em>et al.</em>, +2019</a> grouped by cell type, detailed cell type, project, experiment, etc. +</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=liverMacParland&position=default">Liver +MacParland</a> - This track shows liver expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/30348985/">MacParland<em>et al.</em>, +2018</a> grouped by cell type, broad cell type, and donor.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=lungTravaglini2020&position=default">Lung +Travaglini</a> - This track shows lung expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/33208946/"> Travaglini <em>et al.</em>, +2020</a> binned by categories such as cell type, sample, donor, compartment, +etc. using both 10x and Smart-seq2 library preparation methods.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=muscleDeMicheli&position=default">Muscle De +Micheli</a> - This track shows muscle expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/32624006/">De Micheli <em>et al.</em>, +2020</a> grouped by cell type and sample.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=pancreasBaron&position=default">Pancreas +Baron</a> - This track shows pancreas expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/27667365/">Baron <em>et al.</em>, 2016 +</a> grouped by cell type, detailed cell type, donor, and batch. +</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=placentaVentoTormo&position=default">Placenta +Vento-Tormo</a> - This track shows placenta and matched decidua and maternal +PBMCs expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/30429548/"> Vento-Tormo <em>et al.</em>, +2018</a> grouped by cell type, detailed cell type, stage, etc. using both 10x +and Smart-seq2 library preparation methods.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=rectumWang&position=default">Rectum Wang</a> +- This track shows rectum expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/31753849/"> Wang <em>et al.</em>, +2020</a> grouped by cell type and donor.</li> +<li> +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=skinSoleBoldo&position=default">Skin +Sole-Boldo</a> - This track shows skin expression data from <a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/32327715/"> Solé-Boldo <em>et +al.</em>, 2020</a> grouped by cell type, cell type with donor’s age, donor, and +age.</li> +</ul> +<p> +Many of these datasets can also be explored interactively using the +<a target="_blank" href="http://cells.ucsc.edu/">UCSC Cell Browser</a>. We are +interested in bringing more single-cell datasets into the Genome Browser and +the UCSC Cell Browser as well as the +<a target="_blank" href="http://cells.ucsc.edu/">Human Cell Atlas</a> project. +If you have data you would like to contribute, check out our +<a target="_blank" href="https://docs.google.com/forms/d/e/1FAIpQLSdbr65jBIHwWn3GecJll2RrvxIvzxLikOTIdG17Qzsvs2seig/viewform"> +questionnaire</a>.</p> +<p> +We would like to thank the publication authors for making these data available. +We would also like to thank Jim Kent, Brittney Wick, Luis Nassar, Daniel +Schmelter, Jairo Navarro, and Gerardo Perez for building and testing these +tracks.</p> + <a name="2021"></a> <a name="102821"></a> <h2> Oct. 28, 2021 New GTEx cis-eQTL and RNA-seq read coverage tracks for human (hg38)</h2> <p> We are happy to announce the release of two new tracks for the human assembly (GRCh38/hg38): the <a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gtexEqtlHighConf">GTEx High-Confidence cis-eQTLs from CAVIAR</a> and <a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gtexCov">GTEx RNA-seq read coverage</a> tracks. </p> <dl> <dt>GTEx High-Confidence cis-eQTLs from CAVIAR</dt> <dd> <ul> <li>