GSE62183
shRNA Sensor Analysis of DSIR Selected shRNAs
Purpose: Generate a large, high quality database of paired shRNA efficacy/sequence datapoints. Overall design: Methods:Twelve shRNAs for each Refseq annotated human gene were selected based on the DSIR algorithm. Twelve batches of ~22K shRNAs (corresponding to 12 agilent chips) were then assessed for efficacy via the sensor method outlined in Fellmann et al, Mol Cell, 2011. Conclusions: Neighboring nucleotide combinations are best at predicting shRNA efficacy.