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 @@ + + + + + + +/style/hgGtexTrackSettings.css"> + + + +

Single cell resources at UCSC

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+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: +

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+ UCSC Cell Browser
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Interactively color dimensionality reduction plots by cell annotation or genes
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+ Tabula Muris
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A Genome Browser track showing single cell RNA-seq gene expression, genome coverage and splice sites
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UCSC Cell Browser

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With the Cell Browser + 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. +

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Single cell datasets in the UCSC Genome Browser

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+Below is a screenshot of a +public session +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. +

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