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Nat Methods. 2012 Feb 19;9(4):363-6. doi: 10.1038/nmeth.1898.

A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.

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1
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.

Abstract

Because off-target effects hamper interpretation and validation of RNAi screen data, we developed a bioinformatics method, genome-wide enrichment of seed sequence matches (GESS), to identify candidate off-targeted transcripts in primary screening data. GESS analysis revealed a prominent off-targeted transcript in several screens, including MAD2 (MAD2L1) in a screen for genes required for the spindle assembly checkpoint. GESS analysis results can enhance the validation rate in RNAi screens.

PMID:
22343343
PMCID:
PMC3482495
DOI:
10.1038/nmeth.1898
[Indexed for MEDLINE]
Free PMC Article
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