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Chemical Biology pp 299–318Cite as

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

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Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WEI4152, 1552 University Ave., Madison, WI, 53726, USA

    Jeff S. Piotrowski, Sean J. McIlwain & Irene M. Ong

  2. Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA

    Scott W. Simpkins, Raamesh Deshpande & Chad L. Myers

  3. RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan

    Sheena C. Li

  4. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

    Charlie Boone

  5. Department of Chemistry, University of British Columbia, Vancouver, BC, Canada

    Raymond J. Andersen

Authors
  1. Jeff S. Piotrowski
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  2. Scott W. Simpkins
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  3. Sheena C. Li
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  4. Raamesh Deshpande
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  5. Sean J. McIlwain
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  6. Irene M. Ong
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  7. Chad L. Myers
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  8. Charlie Boone
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  9. Raymond J. Andersen
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Corresponding author

Correspondence to Jeff S. Piotrowski .

Editor information

Editors and Affiliations

  1. Department of Medicine - Cardiovascular Medicine, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Jonathan E. Hempel

  2. Department of Cell and Developmental Biology, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Charles H. Williams

  3. Department of Medicine - Cardiovascular Medicine, Department of Pharmacology, Department of Cell and Developmental Biology, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Charles C. Hong

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Piotrowski, J.S. et al. (2015). Chemical Genomic Profiling via Barcode Sequencing to Predict Compound Mode of Action. In: Hempel, J., Williams, C., Hong, C. (eds) Chemical Biology. Methods in Molecular Biology, vol 1263. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2269-7_23

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  • DOI: https://doi.org/10.1007/978-1-4939-2269-7_23

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2268-0

  • Online ISBN: 978-1-4939-2269-7

  • eBook Packages: Springer Protocols

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