RNA interference (RNAi) has emerged as a powerful technique for studying loss of function phenotypes by specific down-regulation of gene expression, allowing the investigation of virus-host interactions by large scale high-throughput RNAi screens. Here we comprehensively describe a robust and sensitive siRNA screening platform consisting of an experimental setup, single-cell image analysis and statistical as well as bioinformatics analyses. The workflow has been established to elucidate host gene functions exploited by viruses, monitoring both suppression and enhancement of viral replication simultaneously by fluorescence microscopy. The platform comprises a two-stage procedure in which potential host-factors were first identified in a primary screen and afterwards retested in a validation screen to confirm true positive hits. Subsequent bioinformatics analysis allows the identification of cellular genes participating in metabolic pathways and cellular networks utilized by viruses for efficient infection. Our workflow has been used to investigate host factor usage by the human immunodeficiency virus-1 (HIV 1) but can also be adapted to different viruses. Importantly, the provided platform can be used to guide further screening approaches, thus contributing to fill in current gaps in our understanding of virus-host interactions.

@article{FESTBARSPT10,
	author	 = {Kathleen Börner and Johannes Hermle and Christoph Sommer and Nigel P. Brown and Bettina Knapp and Bärbel Glass and Julian Kunkel and Gloria Torralba and Jürgen Reymann and Nina Beil and Jürgen Beneke and Rainer Pepperkok and Reinhard Schneider and Thomas Ludwig and Michael Hausmann and Fred Hamprecht and Holger Erfle and Lars Kaderali and Hans-Georg Kräusslich and Maik J. Lehmann},
	title	 = {{From experimental setup to bioinformatics: an RNAi screening platform to identify host factors involved in HIV-1 replication}},
	year	 = {2010},
	month	 = {01},
	publisher	 = {WILEY-VCH},
	address	 = {Weinheim, Germany},
	journal	 = {Biotechnology Journal},
	series	 = {5-1},
	pages	 = {39--49},
	issn	 = {1860-7314},
	doi	 = {http://dx.doi.org/10.1002/biot.200900226},
	abstract	 = {RNA interference (RNAi) has emerged as a powerful technique for studying loss of function phenotypes by specific down-regulation of gene expression, allowing the investigation of virus-host interactions by large scale high-throughput RNAi screens. Here we comprehensively describe a robust and sensitive siRNA screening platform consisting of an experimental setup, single-cell image analysis and statistical as well as bioinformatics analyses. The workflow has been established to elucidate host gene functions exploited by viruses, monitoring both suppression and enhancement of viral replication simultaneously by fluorescence microscopy. The platform comprises a two-stage procedure in which potential host-factors were first identified in a primary screen and afterwards retested in a validation screen to confirm true positive hits. Subsequent bioinformatics analysis allows the identification of cellular genes participating in metabolic pathways and cellular networks utilized by viruses for efficient infection. Our workflow has been used to investigate host factor usage by the human immunodeficiency virus-1 (HIV 1) but can also be adapted to different viruses. Importantly, the provided platform can be used to guide further screening approaches, thus contributing to fill in current gaps in our understanding of virus-host interactions.},
	url	 = {http://onlinelibrary.wiley.com/doi/10.1002/biot.200900226/pdf},
}