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Open Access Method

A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila

Ramanuj DasGupta1*, Kent Nybakken2, Matthew Booker3, Bernard Mathey-Prevot3, Foster Gonsalves1, Binita Changkakoty1 and Norbert Perrimon34

Author Affiliations

1 New York University School of Medicine/Cancer Institute, Department of Pharmacology, First Avenue, New York, NY 10016, USA

2 Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA, 02472, USA

3 Department of Genetics, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA

4 Howard Hughes Medical Institute, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA

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Genome Biology 2007, 8:R203  doi:10.1186/gb-2007-8-9-r203

Published: 28 September 2007

Abstract

Off-target effects have been demonstrated to be a major source of false-positives in RNA interference (RNAi) high-throughput screens. In this study, we re-assess the previously published transcriptional reporter-based whole-genome RNAi screens for the Wingless and Hedgehog signaling pathways using second generation double-stranded RNA libraries. Furthermore, we investigate other factors that may influence the outcome of such screens, including cell-type specificity, robustness of reporters, and assay normalization, which determine the efficacy of RNAi-knockdown of target genes.