Cell Perturbation Screens for Target Identification by RNAi

  • Kubilay Demir
  • Michael BoutrosEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 910)


Over the last decade, cell-based screening has become a powerful method in target identification and plays an important role both in basic research and drug discovery. The availability of whole genome sequences and improvements in cell-based screening techniques opened new avenues for high-throughput experiments. Large libraries of RNA interference reagents available for many organisms allow the dissection of broad spectrum of cellular processes. Here, we describe the current state of the large-scale phenotype screening with a focus on cell-based screens. We underline the importance and provide details of screen design, scalability, performance, data analysis, and hit prioritization. Similar to classical high-throughput in vitro screens with defined-target approaches in the past, cell-based screens depend on a successful establishment of robust phenotypic assays, the ability to quantitatively measure phenotypic changes and bioinformatics methods for data analysis, integration, and interpretation.

Key words

Functional genomics Drug and RNAi screen design Assay development RNAi libraries Homogeneous and high-content screen analysis Hit prioritization 



The authors would like to thank Julia Gross and Thomas Sandmann for critical comments on the manuscript. This work has been in part supported by NGFN-Plus NeuroNet.


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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Division of Signaling and Functional Genomics, Department for Cell and Molecular Biology, German Cancer Research Center (DKFZ)Heidelberg UniversityHeidelbergGermany

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