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.

Stanford RNAi Research

We have the siARRAY whole human genome siRNA library from Dharmaconpress 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 DOI: 10.1016/j.molcel.2009.06.021 (PDF)

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1. 
Freund A, Zhong FL, Venteicher AS, Meng Z, Veenstra TD, Frydman J, Artandi SE. 
Cell. 2014 Dec 4;159(6):1389-403. Epub 2014 Nov 20. PubMedID: 25467444 PMCID: PMC4329143 DOI: 10.1016/j.cell.2014.10.059

A Human Genome-wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α-XBP1 Activation.
Yang Z, Zhang J, Jiang D, Khatri P, Solow-Cordero DE, Toesca DAS, Koumenis C, Denko NC, Giaccia AJ, Le QT, Koong AC.
Mol Cancer Res. 2018 May;16(5):745-753. Epub 2018 Feb 9.  PubMedID: 29440447 PMCID: PMC5932228 DOI: 10.1158/1541-7786.MCR-17-0307.

Resources for siRNA screeners

Frontiers in RNAi , a publication by the RNAiGlobal Group

Vendor Information:
Dharmacon (now part of Horizon): See David Solow-Cordero for special pricing available to whole genome siRNA screeners.
Qiagen 
Sigma TRC shRNA information 
Genecopoeia 
Transomic Technologies 
Ambion now part of ThermoFisher

Genomics/Software Info:
IACA - Minimum Information About A Cellular Assay 
MIARE - Minimum Information About an RNAi Experiment 
NIH index of Gene Data (ftp://ftp.ncbi.nih.gov/gene/DATA/) 
RefSeq Human Genome Downloads (ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/) 
Harvard Screensaver 
NCBI Databases -US National Library of Medicine
GeneGo/Metacore - Pathway analysis software
NIH Genome 
NIH GenBank 
Ingenuity - Pathway analysis software, now part of Qiagen Bioinformatics
refSeq Converter - Gene Annotation Website (original paper-ID Converter website no longer active)
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 PMCID: PMC3482495 DOI: 10.1038/nmeth.1898

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 DOI: 10.1177/1087057111427348