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

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.

SUBMITTER: Sigoillot FD

PROVIDER: S-EPMC3482495 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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

Sigoillot Frederic D FD Lyman Susan S Huckins Jeremy F JF Adamson Britt B Chung Eunah E Quattrochi Brian B King Randall W RW

Nature methods 20120219 4

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. ...[more]

PMID: 22343343

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