Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ShRNA profiling of human cells containing varying concentrations of shRNA expression constructs to determine shRNA abundance using half hairpin sequences


ABSTRACT: RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. We synthesized DNA microarrays with six overlapping 25 nt long tiling probes complementary to each unique 60 nt molecular barcode sequence associated with every shRNA expression construct. By analyzing dilution series of expression constructs we show how our approach allows quantification of shRNA abundance from a pool and how it clearly outperforms the commonly used analysis via the shRNA’s half hairpin sequences. In this part of the study one equimolar reference pool and three test pools of varying template concentrations were PCR amplified and hybridized to individual arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Boettcher 

PROVIDER: E-MEXP-2475 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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