Recommended Conferences

Human Genetics and Genetic Disorders

Miami, USA

Tissue Engineering and Regenerative Medicine

Chicago, USA
Related Subjects
 

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

Author(s): Sims D, Mendes-Pereira AM, Frankum J, Burgess D, Cerone MA

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.

Similar Articles

Forward RNAi screens in primary human hematopoietic stem/progenitor cells

Author(s): Ali N, Karlsson C, Aspling M, Hu G, Hacohen N, et al.

HMGA2 moderately increases fetal hemoglobin expression in human adult erythroblasts

Author(s): de Vasconcellos JF, Lee YT, Byrnes C, Tumburu L, Miller JL

STAR: Ultrafast universal RNA-seq aligner

Author(s): Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C