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Nucleic Acids Res. 2012 Jan;40(Database issue):D957-63. doi: 10.1093/nar/gkr959. Epub 2011 Nov 18.

COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines.

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1
Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada M5G 0A3.

Abstract

Genome-wide pooled shRNA screens enable global identification of the genes essential for cancer cell survival and proliferation and provide a 'functional genetic' map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting approximately 16,000 human genes and a newly developed scoring approach, we identified essential gene profiles in more than 70 breast, pancreatic and ovarian cancer cell lines. We developed a web-accessible database system for capturing information from each step in our standardized screening pipeline and a gene-centric search tool for exploring shRNA activities within a given cell line or across multiple cell lines. The database consists of a laboratory information and management system for tracking each step of a pooled shRNA screen as well as a web interface for querying and visualization of shRNA and gene-level performance across multiple cancer cell lines. COLT-Cancer Version 1.0 is currently accessible at http://colt.ccbr.utoronto.ca/cancer.

PMID:
22102578
PMCID:
PMC3245009
DOI:
10.1093/nar/gkr959
[Indexed for MEDLINE]
Free PMC Article
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