Second-generation shRNA libraries covering the mouse and human genomes

Silva, J. M., Li, M. Z., Chang, K., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., Sheth, N., Bradshaw, J., Burchard, J., Kulkarni, A., Cavet, G., Sachidanandam, R., McCombie, W. R., Cleary, M. A., Elledge, S. J., Hannon, G. J. (2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet, 37 (11). pp. 1281-8.

URL: http://www.ncbi.nlm.nih.gov/pubmed/16200065
DOI: 10.1038/ng1650

Abstract

Loss-of-function phenotypes often hold the key to understanding the connections and biological functions of biochemical pathways. We and others previously constructed libraries of short hairpin RNAs that allow systematic analysis of RNA interference-induced phenotypes in mammalian cells. Here we report the construction and validation of second-generation short hairpin RNA expression libraries designed using an increased knowledge of RNA interference biochemistry. These constructs include silencing triggers designed to mimic a natural microRNA primary transcript, and each target sequence was selected on the basis of thermodynamic criteria for optimal small RNA performance. Biochemical and phenotypic assays indicate that the new libraries are substantially improved over first-generation reagents. We generated large-scale-arrayed, sequence-verified libraries comprising more than 140,000 second-generation short hairpin RNA expression plasmids, covering a substantial fraction of all predicted genes in the human and mouse genomes. These libraries are available to the scientific community.

Item Type: Paper
Additional Information:
Uncontrolled Keywords: Animals Gene Library Gene Silencing Genome Human Humans Mice genetics MicroRNAs metabolism Plasmids RNA Interference RNA Small Interfering genetics
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNAi
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

organism description > animal > mammal > rodent > mouse
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > siRNA
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL labs > McCombie lab
CSHL labs > Sachidanandam lab
Watson School > Publications
Depositing User: CSHL Librarian
Date Deposited: 05 Jan 2012 19:19
Last Modified: 19 Sep 2014 15:52
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22703

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