Protocol for: Genome-wide shRNA Knockdown Screens Made Easier with DECIPHER
Abstract or Description:
In 2011, Addgene began collaborating with Dr. Alex Chenchik of Cellecta, Inc. and Dr. Gus Frangou of the Fred Hutchinson Cancer Research Center to distribute Cellecta's DECIPHER pooled lentiviral shRNA libraries. The DECIPHER Project was designed to make high-throughput RNAi genetic screening accessible to academia.
Each pooled shRNA library (or module) targets approximately 5,000 genes/transcripts, with 5 to 6 bar-coded shRNAs per target gene to maximize screening efficiency. The library modules were constructed as a series with non-overlapping sets of target genes. There are currently three modules for human and two modules for mouse available which target 15,000 and 10,000 genes, respectively. The first two library modules for human and mouse target mostly well characterized pathway-associated and disease-associated genes. The third human module targets cell surface and DNA-binding proteins, and other conserved genes. Just like Cellecta's custom libraries, the DECIPHER Project libraries are constructed with shRNA expression cassette oligonucleotides containing unique sequence tags ("bar-codes") synthesized on Agilent's array-based platform. Cellecta also offers free bar-code analyzer/deconvoluter software to assist scientists in processing Illumina HT Sequencing data generated from their RNAi screens. For more information about this powerful new screening tool and to request related plasmids contact Addgene, a non-profit plasmid resource.
Posted By: jkamens
on 5/9/2012 1:38:03 PM