2017, CSHL

Transcript:
1. Single-cell genome viewer is a graphical interface, integrating single-cell genomics and conventional pathology of tumors to achieve better-informed clinical decisions.
2. Written in Python, the tool is easily installed and invoked using Anaconda environment.
3. In the opening view, multiple single-cell genomic profiles are represented as columns of a heat map.
4. DNA amplifications are shown in red, and deletions in blue color.
5. The cell genomes are organized as leaves of a genealogical tree.
6. Clones and sub-clones formed by cells are indicated in color in the clone and sub-clone tracks.
7. Additional tracks below the heat map indicate, for each cell, its anatomic sector of origin, the cell sorter gate, and the quality-control measures.
8. Zoom function can be used to examine subsets of cells.
9. Single-cell profiles may be reordered by the sector of origin, making it easier to see which sector harbor clonal populations.
10. Individual sectors may be examined in more detail.
11. Annotated pathology images may be displayed for each sector.
12. Genomic profiles of cells may be selected, individually or in combination, for closer examination as stacked graphs.
13. Genomic regions can be zoomed into...
14. ...and their genomic content examined in the genome browser.


Credit: Alexander Krasnitz, KraJude Kendall, Lubomir Chobardjiev, Vyacheslav Zhygulin, Joan Alexander and Mike Wigler with funding by the National Cancer Institute and the Simons Foundation.

Production: Joan Alexander
Brian Stallard & Andrea Alfano (CSHL Public Affairs)

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