Rapid creation and quantitative monitoring of high coverage shRNA libraries.


Publication Type:

Journal Article

Source:

Nat Methods, Volume 6, Issue 6, p.443-5 (2009)

Keywords:

Base Sequence, Gene Library, Humans, Molecular Sequence Data, Polymerase Chain Reaction, RNA, Messenger, Sequence Analysis, RNA

Abstract:

<p>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.</p>