NAR Molecular Biology Database Collection entry number 817

http://flyRNAi.org/cgi-bin/RNAi_screens.pl

Flockhart I.¹, Booker M.¹, Kiger A.³, Boutros M.⁴, Armknecht S.¹, Ramadan N.¹, Richardson K.¹, Xu A.¹, Perrimon N.^1,2 and Mathey-Prevot B.¹

¹Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA ²Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA ³Department of Biological Sciences, University of California-San Diego, La Jolla, California 92093-0346, USA ⁴German Cancer Research Center, D-69120 Heidelberg, Germany

Contact iflockha@genetics.med.harvard.edu

RNA interference (RNAi) has become a powerful tool for genetic screening in Drosophila. At the Drosophila RNAi Screening Center (DRSC), we are using a library of over 21,000 dsRNAs targeting known and predicted genes in Drosophila. This library is available for the use of visiting scientists wishing to perform full-genome RNAi screens. The data generated from these screens is collected in the DRSC database (http://flyRNAi.org/cgi-bin/RNAi_screens.pl) in a flexible format for the convenience of the scientist and for archiving data. The long-term goal of this database is to provide annotations for as many of the uncharacterized genes in Drosophila as possible. Data from published screens are available to the public through a highly configurable interface that allows detailed examination of the data and provides access to a number of other databases and bioinformatics tools.

Screening at the DRSC Visiting scientists typically perform their screens in duplicate - screening against two full-genome sets. Raw data from duplicate genome sets are collected along with phenotype and "hit" information. The scientists have password-protected accounts which give them access to data entry interfaces and direct links to their personal data, both published and unpublished. The logged in user also has access to some tools for viewing data a plate at a time, direct links to the bioinformatic tools (listed below), and functions for directly querying the quality control (QC) information for the source plates.

Website Overview The public database begins with a page listing all published screens that have been done at the DRSC. From there, the experimental data for each assay may be viewed in a configurable table. Where possible, links to the published papers and supplementary data are also provided. Also on the starting page are links to various informatic tools, a gene lookup function which provides extensive amplicon data, and a list of completed, but not yet published, screens.

The authors would like to thank Carolyn Shamu and Tim Mitchison of The Institute of Chemistry and Cell Biology (ICCB) at Harvard Medical School and Erik Brauner of the Broad Institute for all their help and guidance in setting up the early phase of the DRSC database. We would also like to thank Sara Cherry, Ramanuj Dasgupta, Kent Nybakken, Adam Friedman, Jennifer Philips and the rest of the Perrimon lab for their helpful suggestions on the web interface and feedback on the features of the database. This work was supported by grant R01 GM067761 from the National Institute of the General Medical Sciences. NP is a Howard Hughes Medical Institute investigator.

1. Armknecht, S., Boutros, M., Kiger, A., Nybakken, K., Mathey-Prevot, B. and Perrimon, N. (2005) High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymol, 392, 55-73.
2. Clemens, J.C., Worby, C.A., Simonson-Leff, N., Muda, M., Maehama, T., Hemmings, B.A. and Dixon, J.E. (2000) Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci U S A, 97, 6499-6503.
3. Meister, G. and Tuschl, T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature, 431, 343-349.
4. Hild, M., Beckmann, B., Haas, S.A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F. et al. (2003) An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol, 5, R3. Epub 2003.
5. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195.
6. Agaisse, H., Burrack, L.S., Philips, J., Rubin, E.J., Perrimon, N. and Higgins, D.E. (2005) Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science, 14, 14.
7. Baeg, G.H., Zhou, R. and Perrimon, N. (2005) Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev, 29, 29.
8. Boutros, M., Kiger, A.A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S.A., Consortium, H.F., Paro, R. and Perrimon, N. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science, 303, 832-835.
9. Cherry, S., Doukas, T., Armknecht, S., Whelan, S., Wang, H., Sarnow, P. and Perrimon, N. (2005) Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev, 19, 445-452.
10. DasGupta, R., Kaykas, A., Moon, R.T. and Perrimon, N. (2005) Functional genomic analysis of the Wnt-wingless signaling pathway. Science, 308, 826-833.
11. Eggert, U.S., Kiger, A.A., Richter, C., Perlman, Z.E., Perrimon, N., Mitchison, T.J. and Field, C.M. (2004) Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol, 2, e379. Epub 2004 Oct 2005.
12. Kiger, A., Baum, B., Jones, S., Jones, M., Coulson, A., Echeverri, C. and Perrimon, N. (2003) A functional genomic analysis of cell morphology using RNA interference. J Biol, 2, 27. Epub 2003 Oct 2001.
13. Philips, J.A., Rubin, E.J. and Perrimon, N. (2005) Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection. Science, 14, 14.
14. Qiu, S., Adema, C.M. and Lane, T. (2005) A computational study of off-target effects of RNA interference. Nucleic Acids Res, 33, 1834-1847. Print 2005.
15. Naito, Y., Yamada, T., Matsumiya, T., Ui-Tei, K., Saigo, K. and Morishita, S. (2005) dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Res, 33, W589-591.
16. Gunsalus, K.C., Yueh, W.C., MacMenamin, P. and Piano, F. (2004) RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res, 32 Database issue, D406-410.
17. Arziman, Z., Horn, T. and Boutros, M. (2005) E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res, 33, W582-588.

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