602a1b57a8de2305f98b3cc8a84650fd11fcc45d max Tue May 14 05:32:00 2019 -0700 changes to singlecell page, refs #22679 diff --git src/hg/htdocs/singlecell.html src/hg/htdocs/singlecell.html index bc04904..f1bd996 100755 --- src/hg/htdocs/singlecell.html +++ src/hg/htdocs/singlecell.html @@ -1,107 +1,112 @@ - + /style/hgGtexTrackSettings.css">

Single cell resources at UCSC

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:

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

UCSC Cell Browser

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. + We are happy to add your favorite dataset, contact us at + cells@ucsc.edu. + To set up your own cell browser, follow the instructions at + cellbrowser.readthedocs.org.

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Single cell datasets in the UCSC Genome Browser

Below is a screenshot of a public session -that highlights the Tabula Muris gene expression track +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.