FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

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.

[1]  N. Perrimon,et al.  In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila , 2015, Genetics.

[2]  Yanhui Hu,et al.  FlyRNAi.org—the database of the Drosophila RNAi screening center: 2012 update , 2011, Nucleic Acids Res..

[3]  Randall W. King,et al.  A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens , 2012, Nature Methods.

[4]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[5]  Yanhui Hu,et al.  The Transgenic RNAi Project at Harvard Medical School: Resources and Validation , 2015, Genetics.

[6]  Jim Thurmond,et al.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations , 2014, Nucleic Acids Res..

[7]  Yanhui Hu,et al.  CRISPR guide RNA design for research applications , 2016, The FEBS journal.

[8]  A. Spradling,et al.  Physiological and stem cell compartmentalization within the Drosophila midgut , 2013, eLife.

[9]  Yanhui Hu,et al.  Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis , 2014, BMC Bioinformatics.

[10]  Norbert Perrimon,et al.  FlyRNAi: the Drosophila RNAi screening center database , 2005, Nucleic Acids Res..

[11]  Anushya Muruganujan,et al.  PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium , 2009, Nucleic Acids Res..

[12]  B. Edgar,et al.  Regional Cell-Specific Transcriptome Mapping Reveals Regulatory Complexity in the Adult Drosophila Midgut. , 2015, Cell reports.

[13]  Yanhui Hu,et al.  GLAD: an Online Database of Gene List Annotation for Drosophila , 2015, Journal of genomics.

[14]  Yanli Wang,et al.  PubChem BioAssay: 2014 update , 2013, Nucleic Acids Res..

[15]  N. Perrimon,et al.  Cas9-based genome editing in Drosophila. , 2014, Methods in enzymology.

[16]  Evgeny M. Zdobnov,et al.  OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software , 2014, Nucleic Acids Res..

[17]  Yanhui Hu,et al.  Integrating protein-protein interaction networks with phenotypes reveals signs of interactions , 2013, Nature Methods.

[18]  Suzanna E Lewis,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.

[19]  N. Perrimon,et al.  Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells , 2015, G3: Genes, Genomes, Genetics.

[20]  Gos Micklem,et al.  Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode , 2022 .

[21]  Yanhui Hu,et al.  UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents , 2013, Genetics.

[22]  Yvonne M. Bradford,et al.  ZFIN, The zebrafish model organism database: Updates and new directions , 2015, Genesis.

[23]  Monte Westerfield,et al.  ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics , 2012, Nucleic Acids Res..

[24]  N. Perrimon,et al.  Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi , 2015, Science Signaling.

[25]  Bonnie Berger,et al.  An integrative approach to ortholog prediction for disease-focused and other functional studies , 2011, BMC Bioinformatics.

[26]  N. Perrimon,et al.  Protein Complex–Based Analysis Framework for High-Throughput Data Sets , 2013, Science Signaling.

[27]  Thomas Horn,et al.  GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update , 2012, Nucleic Acids Res..

[28]  N. Perrimon,et al.  High-throughput RNAi screening in cultured cells: a user's guide , 2006, Nature Reviews Genetics.