title: 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.
authors.affiliation: Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Bassik
authors.forename: Robert Jan
authors.initials: RJ
authors.lastname: Lebbink
authors.forename: L Stirling
authors.initials: LS
authors.lastname: Churchman
authors.forename: Nicholas T
authors.initials: NT
authors.lastname: Ingolia
authors.forename: Weronika
authors.initials: W
authors.lastname: Patena
authors.forename: Emily M
authors.initials: EM
authors.lastname: LeProust
authors.forename: Maya
authors.initials: M
authors.lastname: Schuldiner
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Weissman
authors.forename: Michael T
authors.initials: MT
authors.lastname: McManus
mesh_terms: D001483:Base Sequence; D015723:Gene Library; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger