-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: +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

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.

/images/cellbrowser.png">

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.

Single cell resources at UCSC

UCSC Cell Browser

Single cell datasets in the UCSC Genome Browser