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Open Access Research article

Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

Katherine H Fisher2, Victoria M Wright2, Amy Taylor1, Martin P Zeidler2* and Stephen Brown1*

Author Affiliations

1 The Sheffield RNAi Screening Facility, Department of Biomedical Science, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK

2 The MRC Centre for Developmental and Biomedical Genetics and The Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK

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BMC Genomics 2012, 13:506  doi:10.1186/1471-2164-13-506

Published: 24 September 2012

Abstract

Background

Genome-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.

Results

Here 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.

Conclusions

Our 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.

Keywords:
Genome screening; RNAi; Off-target effect; JAK/STAT pathway; Functional genomics; dsRNA