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

Frederic D. Sigoillot, Susan Lyman, Jeremy F. Huckins, Britt Adamson, Eunah Chung, Brian Quattrochi, Randall W. King

Research output: Contribution to journalArticle

105 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)363-366
Number of pages4
JournalNature Methods
Volume9
Issue number4
DOIs
StatePublished - Apr 2012
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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    Sigoillot, F. D., Lyman, S., Huckins, J. F., Adamson, B., Chung, E., Quattrochi, B., & King, R. W. (2012). A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nature Methods, 9(4), 363-366. https://doi.org/10.1038/nmeth.1898