Human Genomic siRNA oligo Libraries at the HTBC
Please contact David Solow-Cordero for a consultation about performing a genomic RNAi knockdown screen. After the consultation, you can fill out the application with the information we will need to commence your screen.
We have the siARRAY whole human genome siRNA library from GE Healthcare (formerly Dharmacon; press release). Stanford is also a member of RNAiglobal. The set consists of pools of 4 oligos per gene. In addition, we have the full genomic upgrade, consisting of each individual siRNA duplex (4 per gene). The set is divided into GPCR (517 genes), Kinase (779), Druggable genome (6022), and the remaining genome (13,804) for a total of 21,122 targeted genes.
We have recently acquired a few copies of the Qiagen Mouse Whole Genome siRNA set V1 against 22,124 gene targets. It is available as pooled aliquots (~4 siRNA per gene target) in 72 X 384 well plates, 33 uL/well of 500 nMolar siRNA.
Please contact David E. Solow-Cordero, Ph.D. if you would like more information on screening with the siRNA libraries.
HTBC siRNA Publications:
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.
Paulsen RD, Soni DV, Wollman R, Hahn AT, Yee MC, Guan A, Hesley JA, Miller SC, Cromwell EF, Solow-Cordero DE, Meyer T, Cimprich KA.
Mol Cell. 2009 Jul 31; 35 (2): 228-39
PubMedID: 19647519 PMCID: PMC2772893 (PDF)
Resources for siRNA screeners:
Frontiers in RNAi, a publication by the RNAiGlobal Group
Vendor Information:
Dharmacon (now part of GE Healthcare): See David Solow-Cordero for special pricing available to whole genome siRNA screeners.
Qiagen
Sigma TRC shRNA information for Stanford researchers
Genecopoeia
Transomic Technologies
Ambion
now part of Life Technologies
Genomics/Software Info:
IACA - Minimum Information About A Cellular Assay
MIARE - Minimum Information About an RNAi Experiment
NIH Gene Data
RefSeq Human Genome Downloads
Harvard Screensaver
Entrez -The Life Sciences Search Engine
GeneGo/Metacore - Pathway analysis software
Genome
GenBank
Ingenuity - Pathway analysis software
ID Converter - Gene Annotation Website
Pathway Studio - Pathway analysis software
Papers on off-target effects:
A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.
Sigoillot FD, Lyman S, Huckins JF, Adamson B, Chung E, Quattrochi B, King RW.
Nat Methods. 2012 Feb 19;9(4):363-6. doi: 10.1038/nmeth.1898.
PubMedID: 22343343
Common seed analysis to identify off-target effects in siRNA screens.
Marine S, Bahl A, Ferrer M, Buehler E.
J Biomol Screen. 2012 Mar;17(3):370-8. Epub 2011 Nov 15.
PubMedID: 22086724
