Author(s): Sims D, Mendes-Pereira AM, Frankum J, Burgess D, Cerone MA
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.
Author(s): Lacalle RA, Pulido D, Vara J, Zaiacaín M, Jiménez A
Author(s): Lanza AM, Kim DS, Alper HS
Author(s): Lee YT, de Vasconcellos JF, Yuan J, Byrnes C, Noh S, et al.
Author(s): Ali N, Karlsson C, Aspling M, Hu G, Hacohen N, et al.
Author(s): de Vasconcellos JF, Lee YT, Byrnes C, Tumburu L, Miller JL
Author(s): Lee YT, de Vasconcellos JF, Byrnes C, Kaushal M, Miller JL
Author(s): Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C
Author(s): Moran DM, Shen H, Maki CG