High-Throughput Drug Screening Facility

In RNAi screening, gene silencing by RNA interference technology is used to identify genes involved in a specific cellular pathway. We perform arrayed, genome-wide RNAi screening using both siRNA duplex– and shRNA hairpin–based technologies.

We have developed an analysis strategy through a stringent, five-step process called the Bhinder-Djaballah (BDA) analysis method. It involves the introduction of the H score as a measure of combined duplex activities toward hit nomination with a minimum score of 60.

In addition, we address off-target effects (OTEs) by performing a comprehensive analysis to eliminate duplexes from the analysis, or by flagging the activities of such duplexes as potential OTEs based on their seed sequence similarities to miRNAs or 3’UTR sequences.

When applied to random RNAi data, the BDA method filters out inherent noise due to the heterogeneous nature of RNAi screening and cell biology.

RNAi Screening Libraries
Below are the different types of libraries we provide for RNAi screening:

• Custom siRNA libraries including the druggable genome, the kinome, DNA damage response genes, and epigenetic genes
• MSKCC collection of siRNA duplexes, which were synthesized using our custom algorithm. This library covers approximately 7,000 human genes with an average coverage of 3 siRNA duplexes per gene.
• The Ambion (Life Technologies) Silencer Select V4.0 Library, which targets 22,000 human genes with an average coverage of 3 siRNA duplexes per gene. The siRNA duplex is chemically modified to help attenuate off-target effects.
• The Mission shRNA Library (The RNAi Consortium, the TRC1 library), purchased from Sigma-Aldrich, consists of 159,000 shRNA constructs targeting both the human and mouse genomes. This library covers approximately 16,000 genes with an average coverage of 5 shRNA hairpins per gene.

All our RNAi screening libraries are arrayed in 384-well microtiter plates.