abaf7f9f1b28276820f73cc81c067f9b4bae6814 bwick Mon Nov 15 08:04:25 2021 -0800 Edited release date for scRNA-seq track group. refs #28378 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index f8e8b3f..f06c671 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,43 +38,44 @@ </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> +<a name="111721"></a> +<h2>Nov. 17, 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> +RNA-seq (scRNA-seq) datasets for the hg38 assembly. Data generated by scRNA-seq +allows us to study the heterogeneity of cells in organs, explore gene expression at +a cellular level, and track cellular states in both development and disease. + <p class ="text-center"> - <img class="text-center" src="../images/newsArchImages/scRNAseq_trackgroup.jpg" width=80%> -</p> + <img class="text-center" src="../images/newsArchImages/scRNAseq.png"></p> <p> -Each new scRNA-seq 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> +We are starting with 14 scRNA-seq tracks covering different major organs of the body. +Each new scRNA-seq 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> @@ -136,61 +137,61 @@ </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> +tracks. In all of the tracks, the gene expression is averaged for each item +in a category.</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" +- 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. @@ -228,31 +229,31 @@ 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 +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