FlyRNAi.org-the Database of the Drosophila RNAi Screening Center and Transgenic RNAi Project: 2017 Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2016 Dec 8

PMID 27924039

Citations 28

Authors

Yanhui Hu

Aram Comjean

Charles Roesel

Arunachalam Vinayagam

Ian Flockhart

Jonathan Zirin

Lizabeth Perkins

Norbert Perrimon

Stephanie E Mohr

Affiliations

Soon will be listed here.

Abstract

The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches.

Citing Articles

eEF1α2 is required for actin cytoskeleton homeostasis in the aging muscle.

Katow H, Ryoo H Dis Model Mech. 2024; 17(9).

PMID: 39207054 PMC: 11381931. DOI: 10.1242/dmm.050729.

Expression of retrotransposons contributes to aging in Drosophila.

Schneider B, Sun S, Lee M, Li W, Skvir N, Neretti N Genetics. 2023; 224(2).

PMID: 37084379 PMC: 10213499. DOI: 10.1093/genetics/iyad073.

Functionally Validating Evolutionary Conserved Risk Genes for Parkinson's Disease in .

Baisgaard A, Koldby K, Kristensen T, Nyegaard M, Rohde P Insects. 2023; 14(2).

PMID: 36835737 PMC: 9958964. DOI: 10.3390/insects14020168.

A large-scale RNAi screen reveals that mitochondrial function is important for meiotic chromosome organization in oocytes.

Nieken K, OBrien K, McDonnell A, Zhaunova L, Ohkura H Chromosoma. 2023; 132(1):1-18.

PMID: 36648541 PMC: 9981535. DOI: 10.1007/s00412-023-00784-9.

pVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes.

Stankovic D, Csordas G, Uhlirova M Life Sci Alliance. 2022; 6(2).

PMID: 36446522 PMC: 9711858. DOI: 10.26508/lsa.202201801.

References

Kriventseva E, Tegenfeldt F, Petty T, Waterhouse R, Simao F, Pozdnyakov I . OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res. 2014; 43(Database issue):D250-6. PMC: 4383991. DOI: 10.1093/nar/gku1220. View

Housden B, Valvezan A, Kelley C, Sopko R, Hu Y, Roesel C . Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal. 2015; 8(393):rs9. PMC: 4642709. DOI: 10.1126/scisignal.aab3729. View

Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T . PubChem BioAssay: 2014 update. Nucleic Acids Res. 2013; 42(Database issue):D1075-82. PMC: 3965008. DOI: 10.1093/nar/gkt978. View

Ruzicka L, Bradford Y, Frazer K, Howe D, Paddock H, Ramachandran S . ZFIN, The zebrafish model organism database: Updates and new directions. Genesis. 2015; 53(8):498-509. PMC: 4545674. DOI: 10.1002/dvg.22868. View

Dutta D, Dobson A, Houtz P, Glasser C, Revah J, Korzelius J . Regional Cell-Specific Transcriptome Mapping Reveals Regulatory Complexity in the Adult Drosophila Midgut. Cell Rep. 2015; 12(2):346-58. DOI: 10.1016/j.celrep.2015.06.009. View

Allan C, Burel J, Moore J, Blackburn C, Linkert M, Loynton S . OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012; 9(3):245-53. PMC: 3437820. DOI: 10.1038/nmeth.1896. View

Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr S . Protein complex-based analysis framework for high-throughput data sets. Sci Signal. 2013; 6(264):rs5. PMC: 3756668. DOI: 10.1126/scisignal.2003629. View

Housden B, Lin S, Perrimon N . Cas9-based genome editing in Drosophila. Methods Enzymol. 2014; 546:415-39. DOI: 10.1016/B978-0-12-801185-0.00019-2. View

Flockhart I, Booker M, Hu Y, McElvany B, Gilly Q, Mathey-Prevot B . FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res. 2011; 40(Database issue):D715-9. PMC: 3245182. DOI: 10.1093/nar/gkr953. View

10.

Marianes A, Spradling A . Physiological and stem cell compartmentalization within the Drosophila midgut. Elife. 2013; 2:e00886. PMC: 3755342. DOI: 10.7554/eLife.00886. View

11.

Yilmazel B, Hu Y, Sigoillot F, Smith J, Shamu C, Perrimon N . Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. BMC Bioinformatics. 2014; 15:192. PMC: 4073188. DOI: 10.1186/1471-2105-15-192. View

12.

Mohr S, Hu Y, Rudd K, Buckner M, Gilly Q, Foster B . Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. G3 (Bethesda). 2015; 5(9):1919-24. PMC: 4555228. DOI: 10.1534/g3.115.019364. View

13.

Mohr S, Hu Y, Ewen-Campen B, Housden B, Viswanatha R, Perrimon N . CRISPR guide RNA design for research applications. FEBS J. 2016; 283(17):3232-8. PMC: 5014588. DOI: 10.1111/febs.13777. View

14.

Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, Samsonova A . Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2013; 11(1):94-9. PMC: 3877743. DOI: 10.1038/nmeth.2733. View

15.

Roy S, Ernst J, Kharchenko P, Kheradpour P, Negre N, Eaton M . Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010; 330(6012):1787-97. PMC: 3192495. DOI: 10.1126/science.1198374. View

16.

Perkins L, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K . The Transgenic RNAi Project at Harvard Medical School: Resources and Validation. Genetics. 2015; 201(3):843-52. PMC: 4649654. DOI: 10.1534/genetics.115.180208. View

17.

Schmidt E, Pelz O, Buhlmann S, Kerr G, Horn T, Boutros M . GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 2012; 41(Database issue):D1021-6. PMC: 3531141. DOI: 10.1093/nar/gks1170. View

18.

Flockhart I, Booker M, Kiger A, Boutros M, Armknecht S, Ramadan N . FlyRNAi: the Drosophila RNAi screening center database. Nucleic Acids Res. 2005; 34(Database issue):D489-94. PMC: 1347476. DOI: 10.1093/nar/gkj114. View

19.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas P . PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2009; 38(Database issue):D204-10. PMC: 2808919. DOI: 10.1093/nar/gkp1019. View

20.

Lin S, Ewen-Campen B, Ni X, Housden B, Perrimon N . In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila. Genetics. 2015; 201(2):433-42. PMC: 4596659. DOI: 10.1534/genetics.115.181065. View