Variations in genome-wide RNAi screens: lessons from influenza research

  • Yu-Chi Chou National RNAi Core Facility Platform, Academia Sinica, Taipei 11529, Taiwan. Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
  • Michael MC Lai Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan. Research Center for Emerging Viruses, China Medical University Hospital, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung 40402, Taiwan. China Medical University, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung 40402, Taiwan. Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan
  • Yi-Chen Wu National RNAi Core Facility Platform, Academia Sinica, Taipei 11529, Taiwan
  • Nai-Chi Hsu National RNAi Core Facility Platform, Academia Sinica, Taipei 11529, Taiwan
  • King-Song Jeng National RNAi Core Facility Platform, Academia Sinica, Taipei 11529, Taiwan. Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
  • Wen-Chi Su Research Center for Emerging Viruses, China Medical University Hospital, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung 40402, Taiwan. China Medical University, Room 602, 6 F, Cancer Center Building, No. 6, Hsueh-Shih Road, Taichung 40402, Taiwan
DOI: 10.1186/s13336-015-0017-5

Abstract

Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screening strategies. To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication. However, the host factors identified by different research groups are not always consistent. Taking influenza virus screens as an example, we found that a number of screening parameters may directly or indirectly influence the primary hits identified by the screens. This review highlights the differences among the published genome-wide screening approaches and offers recommendations for performing a good pooled shRNA screen/selection.

Keywords

RNA interference (RNAi), Genome-wide screen, Arrayed siRNA screen, Pooled shRNA screen, Influenza virus, Lentivirus
Published
2015-03-03
How to Cite
CHOU, Yu-Chi et al. Variations in genome-wide RNAi screens: lessons from influenza research. Journal of Clinical Bioinformatics, [S.l.], v. 5, n. 1, mar. 2015. ISSN 2043-9113. Available at: <http://jclinbioinformatics.com/article/view/57>. Date accessed: 18 nov. 2017. doi: https://doi.org/10.1186/s13336-015-0017-5.