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Rapid creation and quantitative monitoring of high coverage shRNA libraries.

ABSTRACT: Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per 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 true hits.

SUBMITTER: Bassik MC

PROVIDER: S-EPMC2783737 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Bassik Michael C MC Lebbink Robert Jan RJ Churchman L Stirling LS Ingolia Nicholas T NT Patena Weronika W LeProust Emily M EM Schuldiner Maya M Weissman Jonathan S JS McManus Michael T MT

Nature methods 20090517 6

Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per 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 true hits. ...[more]

PMID: 19448642

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