Decoding pooled RNAi screens by means of barcode tiling arrays.

ABSTRACT:

Background

RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. In the past years, several pooled large-scale shRNA screens have identified a variety of genes involved in cancer cell proliferation. All of those studies employed microarray analysis, utilizing either the shRNA's half hairpin sequence or an additional shRNA-associated 60 nt barcode sequence as a molecular tag. Here we describe a novel method to decode pooled RNAi screens, namely barcode tiling array analysis, and demonstrate how this approach can be used to precisely quantify the abundance of individual shRNAs from a pool.

Results

We synthesized DNA microarrays with six overlapping 25 nt long tiling probes compleme

SUBMITTER: Boettcher M 

PROVIDER: S-EPMC2824726 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature