Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm.

ABSTRACT: In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS) deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that suc

SUBMITTER: Schaefer C 

PROVIDER: S-EPMC5792015 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature