3d9ee83a5687500fb54e6894b17e0331f413d1e1 max Mon May 13 05:28:43 2019 -0700 adding first version of single cell static page, refs #22679 diff --git src/hg/htdocs/singlecell.html src/hg/htdocs/singlecell.html new file mode 100755 index 0000000..bc04904 --- /dev/null +++ src/hg/htdocs/singlecell.html @@ -0,0 +1,107 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="GTEx Resources at UCSC" --> +<!--#set var="ROOT" value="." --> + +<!--#include virtual="$ROOT/inc/gbPageStart.html"--> + +<link rel="stylesheet" href="<!--#echo var="ROOT" -->/style/hgGtexTrackSettings.css"> + +<style> +.gbsPage dl { + padding-left: 60px; +} + +.gbsPage dt { + float: left; + clear: left; + width: 250px; + margin-top: 0; + padding: 0 0 0.5em 0; +} +.gbsPage dd { + margin: 0 0 0 200px; + padding: 0 0 0.5em 0; +} + +.gbsPage dl dt { + position: relative; +} + +.gbsPage dl dt::before { /* square bullets, from hgGateway */ + position: absolute; + top: 0.4em; + left: -1em; + width: 8px; + height: 8px; + background-color: #7e1f16; /* dark red */ + content: ''; +} + +.gbsPage dl.gbsNoBullet dt::before { + content: none; +} + +</style> + +<h1>Single cell resources at UCSC</h1> +<p> +Single cell experiments measure thousands of gene loci in thousands of cells at +the same time. It is challenging explore and share these high-dimensional data. +The UCSC Genome Browser is adding published datasets as tracks and a new +visualisation tool: +</p> +<p> +<dl> +<dt><a target="_blank" + href="https://cells.ucsc.edu"> + UCSC Cell Browser</a></dt> + <dd>Interactively color dimensionality reduction plots by cell annotation or genes</dd> +<dt><a target="_blank" + href="../cgi-bin/hgTrackUi?db=mm10&g=tabulaMuris"> + Tabula Muris</a></dt> + <dd>A Genome Browser track showing single cell RNA-seq gene expression, genome coverage and splice sites</dd> +</dl> + +<div class="row"> + <div class="col-md-6"> + <h2>UCSC Cell Browser</h2> + <p>With the <a target=_blank href="https://cells.ucsc.edu">Cell Browser</a> + you can plot cells arranged by algorithms like t-SNE or UMAP. Color + these by annotated meta data or genes via the left side bar. Select + cells via the legend on the right or with the rectangle selection tool. + You can export the current cell selection or annotate it via the "Tools" menu. +</p> + <p class="text-center"> + <a target=_blank href="https://cells.ucsc.edu" alt="Screenshot of UCSC Cell Browser"> + <img style="width:100%" src="<!--#echo var="ROOT" -->/images/cellbrowser.png"> + </a> + </p> + </div> + <div class="col-md-6"> + <h2>Single cell datasets in the UCSC Genome Browser</h2> + <p> +Below is a screenshot of a +<a target="_blank" +href="http://genome.ucsc.edu/s/Max/tabMuris">public session</a> +that highlights the Tabula Muris gene expression track +The session shows the Sox10 locus. The gene expression track at the top shows that the +gene is only well expressed in basal cells (orange), mammary gland (blue) and oligodendrocytes (pink). +These cell type names are shown when you hover with the mouse over the bars on +the genome browser. The coverage tracks below show that all exons are +transcribed in these, but the last exon is also transcribed in stromal cells +and some non-coding transcription is seen in goblet cells 3' of the gene. The +splicing tracks below show that proper splicing is limited to the four cell types +described above. This is also a non-coding region conserved in zebrafish and chicken. + <p class="text-center"> + <a target="_blank" href="http://genome.ucsc.edu/s/Max/tabMuris" alt="genome browser session link"> + <img src="../images/screenshot-tabMuris.png" style='width:100%'> + </a> + </p> + </div> +</div> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html"--> + +<script type='text/javascript' src='/js/hgGtexTrackSettings.js'></script> + +