Design and evaluation of genome-wide libraries for RNA interference screens

Thomas Horn; Thomas Sandmann; Michael Boutros

doi:10.1186/gb-2010-11-6-r61

Design and evaluation of genome-wide libraries for RNA interference screens

Genome Biol. 2010;11(6):R61. doi: 10.1186/gb-2010-11-6-r61. Epub 2010 Jun 15.

Authors

Thomas Horn¹, Thomas Sandmann, Michael Boutros

Affiliation

¹ German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and University of Heidelberg, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.

Abstract

RNA interference (RNAi) screens have enabled the systematic analysis of many biological processes in cultured cells and whole organisms. The success of such screens and the interpretation of the data depend on the stringent design of RNAi libraries. We describe and validate NEXT-RNAi, a software for the automated design and evaluation of RNAi sequences on a genome-wide scale. NEXT-RNAi is implemented as open-source software and is accessible at http://www.nextrnai.org/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Anopheles / genetics
Computational Biology / methods*
Drosophila melanogaster / enzymology
Drosophila melanogaster / genetics
Gene Knockdown Techniques
Genome / genetics*
Genome, Human / genetics
Genomic Library*
Humans
Phosphoprotein Phosphatases / metabolism
Quality Control
RNA Interference*
RNA, Small Interfering / metabolism
Reproducibility of Results
Software*
Tribolium / genetics

Substances

RNA, Small Interfering
Phosphoprotein Phosphatases