Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries

Short hairpin RNA (shRNA) libraries are limited by the low efficacy of many shRNAs, giving false negatives, and off-target effects, giving false positives. Here we present a strategy for rapidly creating expanded shRNA pools (∼30 shRNAs/gene) that are analyzed by deep-sequencing (EXPAND). This appro...

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Detalles Bibliográficos
Autores principales: Bassik, Michael C., Lebbink, Robert Jan, Churchman, L. Stirling, Ingolia, Nicholas T., Patena, Weronika, LeProust, Emily M., Schuldiner, Maya, Weissman, Jonathan S., McManus, Michael T.
Formato: Texto
Lenguaje:English
Publicado: 2009
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783737/
https://www.ncbi.nlm.nih.gov/pubmed/19448642
http://dx.doi.org/10.1038/nmeth.1330
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author Bassik, Michael C.
Lebbink, Robert Jan
Churchman, L. Stirling
Ingolia, Nicholas T.
Patena, Weronika
LeProust, Emily M.
Schuldiner, Maya
Weissman, Jonathan S.
McManus, Michael T.
author_facet Bassik, Michael C.
Lebbink, Robert Jan
Churchman, L. Stirling
Ingolia, Nicholas T.
Patena, Weronika
LeProust, Emily M.
Schuldiner, Maya
Weissman, Jonathan S.
McManus, Michael T.
author_sort Bassik, Michael C.
collection PubMed
description Short hairpin RNA (shRNA) libraries are limited by the low efficacy of many shRNAs, giving false negatives, and off-target effects, giving false positives. Here we present a strategy for rapidly creating expanded shRNA pools (∼30 shRNAs/gene) that are analyzed by deep-sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of whether a gene is a true hit.
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spelling pubmed-27837372009-12-01 Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries Bassik, Michael C. Lebbink, Robert Jan Churchman, L. Stirling Ingolia, Nicholas T. Patena, Weronika LeProust, Emily M. Schuldiner, Maya Weissman, Jonathan S. McManus, Michael T. Nat Methods Article Short hairpin RNA (shRNA) libraries are limited by the low efficacy of many shRNAs, giving false negatives, and off-target effects, giving false positives. Here we present a strategy for rapidly creating expanded shRNA pools (∼30 shRNAs/gene) that are analyzed by deep-sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of whether a gene is a true hit. 2009-05-17 2009-06 /pmc/articles/PMC2783737/ /pubmed/19448642 http://dx.doi.org/10.1038/nmeth.1330 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download 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
Bassik, Michael C.
Lebbink, Robert Jan
Churchman, L. Stirling
Ingolia, Nicholas T.
Patena, Weronika
LeProust, Emily M.
Schuldiner, Maya
Weissman, Jonathan S.
McManus, Michael T.
Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title_full Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title_fullStr Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title_full_unstemmed Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title_short Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries
title_sort rapid creation and quantitative monitoring of high coverage shrna libraries
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783737/
https://www.ncbi.nlm.nih.gov/pubmed/19448642
http://dx.doi.org/10.1038/nmeth.1330
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