Measuring genetic interactions in human cells by RNAi and imaging

Nature Protocols

Volumn 9, Issue 10, 2014, Pages 2341-2353

  Laufer, Christina ^a,b   Fischer, Bernd ^c   Huber, Wolfgang ^c   Boutros, Michael ^a,b  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; CELL COUNTING; CONTROLLED STUDY; GENE INTERACTION; GENE MAPPING; GENE SILENCING; GENOTYPE; HUMAN; HUMAN CELL; IMAGE ANALYSIS; PHENOTYPE; PRIORITY JOURNAL; RNA INTERFERENCE;

EID: 84964221826     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.160     Document Type: Article

References (20)

1. Manolio, T.A. et al. Finding the missing heritability of complex diseases. Nature 461, 747-753 (2009).
2. Bandyopadhyay, S. et al. Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389 (2010).
3. Baryshnikova, A. et al. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat. Methods 7, 1017-1024 (2010).
4. Dixon, S.J., Costanzo, M., Baryshnikova, A., Andrews, B. & Boone, C. Systematic mapping of genetic interaction networks. Annu. Rev. Genet. 43, 601-625 (2009).
5. Nichols, R.J. et al. Phenotypic landscape of a bacterial cell. Cell 144, 143-156 (2011).
6. Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425-431 (2010).
7. Horn, T. et al. Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat. Methods 8, 341-346 (2011).
8. Laufer, C., Fischer, B., Billmann, M., Huber, W. & Boutros, M. Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nat. Methods 10, 427-431 (2013).
9. Casey, F.P., Cagney, G., Krogan, N.J. & Shields, D.C. Optimal stepwise experimental design for pairwise functional interaction studies. Bioinformatics 24, 2733-2739 (2008).
10. Bassik, M.C. et al. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 152, 909-922 (2013).
11. Roguev, A. et al. Quantitative genetic-interaction mapping in mammalian cells. Nat. Methods 10, 432-437 (2013).
12. Hart, T. & Moffat, J. Scaling up the systematic hunt for mammalian genetic interactions. Nat. Methods 10, 397-399 (2013).
13. Fuchs, F. et al. Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol. Syst. Biol. 6, 370 (2010).
14. Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
15. Pau, G., Fuchs, F., Sklyar, O., Boutros, M. & Huber, W. EBImage-an R package for image processing with applications to cellular phenotypes. Bioinformatics 26, 979-981 (2010).
16. Boutros, M., Bras, L.P. & Huber, W. Analysis of cell-based RNAi screens. Genome Biol. 7, R66 (2006).
17. Axelsson, E. et al. Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. BMC Bioinformatics 12, 342 (2011).
18. Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3 (2004).
19. Jones, T., Carpenter, A. & Golland, P. Voronoi-based segmentation of cells on image manifolds. in CVBIA '05: Proceedings of the First International Conference on Computer Vision for Biomedical Image Applications 535-543 (Springer-Verlag 2005).
20. Mani, R., St Onge, R.P., Hartman, J.L.t., Giaever, G. & Roth, F.P. Defining genetic interaction. Proc. Natl. Acad. Sci. USA 105, 3461-3466 (2008).