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Chemical Genomic Profiling via Barcode Sequencing to Predict Compound Mode of Action

  • Jeff S. PiotrowskiEmail author
  • Scott W. Simpkins
  • Sheena C. Li
  • Raamesh Deshpande
  • Sean J. McIlwain
  • Irene M. Ong
  • Chad L. Myers
  • Charlie Boone
  • Raymond J. Andersen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1263)

Abstract

Chemical genomics is an unbiased, whole-cell approach to characterizing novel compounds to determine mode of action and cellular target. Our version of this technique is built upon barcoded deletion mutants of Saccharomyces cerevisiae and has been adapted to a high-throughput methodology using next-generation sequencing. Here we describe the steps to generate a chemical genomic profile from a compound of interest, and how to use this information to predict molecular mechanism and targets of bioactive compounds.

Key words

Chemical genomics Barcode sequencing Functional genomics Yeast deletion collection 

Notes

Acknowledgements

J.P., S.M., and I.O. are funded by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494). SC is supported by a RIKEN Foreign Postdoctoral Researcher Award. C.M., and R.D. are supported by grants from the National Institutes of Health (1R01HG005084-01A1, 1R01GM104975-01, R01HG005853), a grant from the National Science Foundation (DBI 0953881), and the CIFAR Genetic Networks Program. S.W.S. is supported by an NIH Biotechnology training grant (5T32GM008347-22). C.B. is supported by the Canadian Institutes of Health Research (CIHR MOP-57830). R.A. is supported by the Natural Science and Engineering Research Council (NSERC) of Canada, the Canada Foundation for Innovation (CFI), and the Canadian Cancer Society Research Institute.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Jeff S. Piotrowski
    • 1
    Email author
  • Scott W. Simpkins
    • 2
  • Sheena C. Li
    • 3
  • Raamesh Deshpande
    • 2
  • Sean J. McIlwain
    • 1
  • Irene M. Ong
    • 1
  • Chad L. Myers
    • 2
  • Charlie Boone
    • 4
  • Raymond J. Andersen
    • 5
  1. 1.Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Department of Computer Science and EngineeringUniversity of Minnesota-Twin CitiesMinneapolisUSA
  3. 3.RIKEN Center for Sustainable Resource ScienceWakoJapan
  4. 4.Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
  5. 5.Department of ChemistryUniversity of British ColumbiaVancouverCanada

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