A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens

Because off-target effects hamper interpretation and validation of RNAi screens, we developed a bioinformatics method, Genome-wide Enrichment of Seed Sequence matches (GESS), to identify candidate off-targeted transcripts from direct analysis of primary screening data. GESS identified a prominent of...

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Autores principales: Sigoillot, Frederic D., Lyman, Susan, Huckins, Jeremy F., Adamson, Britt, Chung, Eunah, Quattrochi, Brian, King, Randall W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2012
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482495/
https://www.ncbi.nlm.nih.gov/pubmed/22343343
http://dx.doi.org/10.1038/nmeth.1898
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author Sigoillot, Frederic D.
Lyman, Susan
Huckins, Jeremy F.
Adamson, Britt
Chung, Eunah
Quattrochi, Brian
King, Randall W.
author_facet Sigoillot, Frederic D.
Lyman, Susan
Huckins, Jeremy F.
Adamson, Britt
Chung, Eunah
Quattrochi, Brian
King, Randall W.
author_sort Sigoillot, Frederic D.
collection PubMed
description Because off-target effects hamper interpretation and validation of RNAi screens, we developed a bioinformatics method, Genome-wide Enrichment of Seed Sequence matches (GESS), to identify candidate off-targeted transcripts from direct analysis of primary screening data. GESS identified a prominent off-targeted transcript in several screens, including MAD2 in a screen for components of the spindle assembly checkpoint. We demonstrate how incorporation of the results of GESS analysis can enhance the validation rate in RNAi screens.
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spelling pubmed-34824952012-10-28 A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens Sigoillot, Frederic D. Lyman, Susan Huckins, Jeremy F. Adamson, Britt Chung, Eunah Quattrochi, Brian King, Randall W. Nat Methods Article Because off-target effects hamper interpretation and validation of RNAi screens, we developed a bioinformatics method, Genome-wide Enrichment of Seed Sequence matches (GESS), to identify candidate off-targeted transcripts from direct analysis of primary screening data. GESS identified a prominent off-targeted transcript in several screens, including MAD2 in a screen for components of the spindle assembly checkpoint. We demonstrate how incorporation of the results of GESS analysis can enhance the validation rate in RNAi screens. 2012-02-19 /pmc/articles/PMC3482495/ /pubmed/22343343 http://dx.doi.org/10.1038/nmeth.1898 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Sigoillot, Frederic D.
Lyman, Susan
Huckins, Jeremy F.
Adamson, Britt
Chung, Eunah
Quattrochi, Brian
King, Randall W.
A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title_full A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title_fullStr A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title_full_unstemmed A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title_short A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens
title_sort bioinformatics method identifies prominent off-targeted transcripts in rnai screens
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482495/
https://www.ncbi.nlm.nih.gov/pubmed/22343343
http://dx.doi.org/10.1038/nmeth.1898
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