ArticleBMC genomics2012
Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Chinmo is a novel regulator of differential Hippo signaling response within a single developing organ.bioRxiv : the preprint server for biology · 2025Article
- Article
- Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice.Nature communications · 2022Article
- Drosophila Jak/STAT Signaling: Regulation and Relevance in Human Cancer and Metastasis.International journal of molecular sciences · 2018Review
- Characterization of aBiology open · 2018Article
- A genome-wide RNAi screen identifies MASK as a positive regulator of cytokine receptor stability.Journal of cell science · 2018Article
- Autosomal dominant retinitis pigmentosa-associated gene PRPF8 is essential for hypoxia-induced mitophagy through regulating ULK1 mRNA splicing.Autophagy · 2018Article
- Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development.Nature genetics · 2016Article
- Mechanisms of JAK/STAT pathway negative regulation by the short coreceptor Eye Transformer/Latran.Molecular biology of the cell · 2016Article
- Methotrexate Is a JAK/STAT Pathway Inhibitor.PloS one · 2015Article
- RNAi screening in Drosophila cells and in vivo.Methods (San Diego, Calif.) · 2014Review
- Genome-wide RNAi screen identifies the Parkinson disease GWAS risk locus SREBF1 as a regulator of mitophagy.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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5 authors.
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Abstract
backgroundGenome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated.
resultsHere we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols.
conclusionsOur work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens.
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