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High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing.

ABSTRACT: RNA interference (RNAi) screening is a state-of-the-art technology that enables the dissection of biological processes and disease-related phenotypes. The commercial availability of genome-wide, short hairpin RNA (shRNA) libraries has fueled interest in this area but the generation and analysis of these complex data remain a challenge. Here, we describe complete experimental protocols and novel open source computational methodologies, shALIGN and shRNAseq, that allow RNAi screens to be rapidly deconvoluted using next generation sequencing. Our computational pipeline offers efficient screen analysis and the flexibility and scalability to quickly incorporate future developments in shRNA library technology.

SUBMITTER: Sims D

PROVIDER: S-EPMC3333774 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing.

Sims David D Mendes-Pereira Ana M AM Frankum Jessica J Burgess Darren D Cerone Maria-Antonietta MA Lombardelli Cristina C Mitsopoulos Costas C Hakas Jarle J Murugaesu Nirupa N Isacke Clare M CM Fenwick Kerry K Assiotis Ioannis I Kozarewa Iwanka I Zvelebil Marketa M Ashworth Alan A Lord Christopher J CJ

Genome biology 20111021 10

RNA interference (RNAi) screening is a state-of-the-art technology that enables the dissection of biological processes and disease-related phenotypes. The commercial availability of genome-wide, short hairpin RNA (shRNA) libraries has fueled interest in this area but the generation and analysis of these complex data remain a challenge. Here, we describe complete experimental protocols and novel open source computational methodologies, shALIGN and shRNAseq, that allow RNAi screens to be rapidly d ...[more]

PMID: 22018332

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