GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update

Schmidt, Esther; Pelz, Oliver; Buhlmann, Svetlana; Kerr, Gráinne; Horn, Thomas; Boutros, Michael

doi:10.1093/nar/gks1170

Cited by 131 publications

(123 citation statements)

References 23 publications

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“…To date, more than 100 genome-wide screens have been conducted, including for components of diverse signaling pathways and cell biological processes, among others (Flockhart et al 2012;Schmidt et al 2013). Such studies illustrate how Drosophila cell lines can be used to discover novel gene functions and understand cellular behaviors, knowledge that can direct in vivo studies .…”

mentioning

confidence: 99%

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

et al. 2014

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We expanded the knowledge base for Drosophila cell line transcriptomes by deeply sequencing their small RNAs. In total, we analyzed more than 1 billion raw reads from 53 libraries across 25 cell lines. We verify reproducibility of biological replicate data sets, determine common and distinct aspects of miRNA expression across cell lines, and infer the global impact of miRNAs on cell line transcriptomes. We next characterize their commonalities and differences in endo-siRNA populations. Interestingly, most cell lines exhibit enhanced TE-siRNA production relative to tissues, suggesting this as a common aspect of cell immortalization. We also broadly extend annotations of cis-NAT-siRNA loci, identifying ones with common expression across diverse cells and tissues, as well as cell-restricted loci. Finally, we characterize small RNAs in a set of ovary-derived cell lines, including somatic cells (OSS and OSC) and a mixed germline/somatic cell population (fGS/ OSS) that exhibits ping-pong piRNA signatures. Collectively, the ovary data reveal new genic piRNA loci, including unusual configurations of piRNA-generating regions. Together with the companion analysis of mRNAs described in a previous study, these small RNA data provide comprehensive information on the transcriptional landscape of diverse Drosophila cell lines. These data should encourage broader usage of fly cell lines, beyond the few that are presently in common usage.

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confidence: 99%

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

et al. 2014

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“…Some of the dsRNAs were prepared using a library (Foley and O'Farrell 2004) that was kindly provided by Steve Rogers. Other dsRNAs were synthesized from PCR-generated templates, which were prepared by using genomic DNA and gene-specific primers described in the GenomeRNAi database (Schmidt et al 2013). The dsRNA-treated cells were harvested and heat-shocked at 32°C prior to RNA extraction and Northern blot analysis.…”

Section: Rnai-mediated Protein Depletion In Cultured Cellsmentioning

confidence: 99%

Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination

Brewer-Jensen

Wilson

Abernethy

et al. 2015

RNA

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Although RNA polymerase II (Pol II) productively transcribes very long genes in vivo, transcription through extragenic sequences often terminates in the promoter-proximal region and the nascent RNA is degraded. Mechanisms that induce early termination and RNA degradation are not well understood in multicellular organisms. Here, we present evidence that the suppressor of sable [su(s)] regulatory pathway of Drosophila melanogaster plays a role in this process. We previously showed that Su(s) promotes exosome-mediated degradation of transcripts from endogenous repeated elements at an Hsp70 locus (Hsp70-αβ elements). In this report, we identify Wdr82 as a component of this process and show that it works with Su(s) to inhibit Pol II elongation through Hsp70-αβ elements. Furthermore, we show that the unstable transcripts produced during this process are polyadenylated at heterogeneous sites that lack canonical polyadenylation signals. We define two distinct regions that mediate this regulation. These results indicate that the Su(s) pathway promotes RNA degradation and transcription termination through a novel mechanism.

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“…FlyFISH and other expression data can also be viewed and navigated at FlyExpress (Kumar et al 2011) ( Table 4). Several resources facilitate search and view of cell-based and in vivo data relevant to RNAi screens, with online entry points to various datasets available through websites such as the DRSC (Flockhart et al 2012) and GenomeRNAi (Schmidt et al 2013) (for URLs see Table 4). The RSVP search tool for search and view of in vivo RNAi data is somewhat unique in that it allows users not just to view text but when available, also to view example images of mutant phenotypes.…”

Section: Data Search and View At Metasitesmentioning

confidence: 99%

“…Tools like UP-TORR and FlyPrimerBank can be used to help identify in vivo fly stocks for follow-up studies and design primers for qPCR validation of knockdown. Finally, after publication, the screen data are shared with the community through the DRSC (flyrnai.org), where they are subsequently captured by GenomeRNAi (Schmidt et al 2013) and other metasites.…”

Section: Example Functional Genomics Workflowsmentioning

confidence: 99%

Resources for Functional Genomics Studies in Drosophila melanogaster

Mohr

Kim

et al. 2014

Genetics

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Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, "meta" information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large-and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.

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GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update

Cited by 131 publications

References 23 publications

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination

Resources for Functional Genomics Studies in Drosophila melanogaster

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