84fff89cc215a064df57b22b843ddece6c0e1739 mspeir Thu Jun 20 03:12:17 2019 -0700 Tweaks to cell browser section. Minor white space formatting of Tabula Muris section. refs #22679 diff --git src/hg/htdocs/singlecell.html src/hg/htdocs/singlecell.html index 2199460..8d6137e 100755 --- src/hg/htdocs/singlecell.html +++ src/hg/htdocs/singlecell.html @@ -1,115 +1,126 @@ /style/hgGtexTrackSettings.css">

Single cell resources at UCSC

Single cell experiments measure tens of thousands of gene loci in thousands of cells at the same time. That resulting data is challenging to visualize. The UCSC Genome Browser is adding published datasets as tracks and an entirely new data exploration tool:

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

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

+ The UCSC Cell Browser + is a fast, lightweight viewer for single-cell data. You can: +

+ Contact us at + + cells@ucsc. + edu to request new datasets or suggest improvements. + + To set up your own cell browser, follow our installation and set up instructions.

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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. 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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