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Barcode Sequencing for Understanding Drug–Gene Interactions

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Bioinformatics and Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 910))

Abstract

With the advent of next-generation sequencing (NGS) technology, methods previously developed for microarrays have been adapted for use by NGS. Here we describe in detail a protocol for Barcode analysis by sequencing (Bar-seq) to assess pooled competitive growth of individually barcoded yeast deletion mutants. This protocol has been optimized on two sequencing platforms: Illumina’s Genome Analyzer IIx/HiSeq2000 and Life Technologies SOLiD3/5500. In addition, we provide guidelines for assessment of human knockdown cells using short-hairpin RNAs (shRNA) and an Illumina sequencing readout.

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Acknowledgements

A.M.S. is supported by a University of Toronto Open Fellowship. Research in the Giaever and Nislow laboratories is supported by the NHGRI and CIHR.

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Authors and Affiliations

  1. Donnelly Centre, University of Toronto, Toronto, ON, Canada

    Andrew M. Smith, Tanja Durbic, Saranya Kittanakom, Guri Giaever & Corey Nislow

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  1. Andrew M. Smith
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  2. Tanja Durbic
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  3. Saranya Kittanakom
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  4. Guri Giaever
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  5. Corey Nislow
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Correspondence to Corey Nislow .

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Editors and Affiliations

  1. , Department of Pathology, The University of New Mexico, Camino de Salud 915, Albuquerque, 87131, New Mexico, USA

    Richard S. Larson

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Smith, A.M., Durbic, T., Kittanakom, S., Giaever, G., Nislow, C. (2012). Barcode Sequencing for Understanding Drug–Gene Interactions. In: Larson, R. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 910. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-965-5_4

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  • DOI: https://doi.org/10.1007/978-1-61779-965-5_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-964-8

  • Online ISBN: 978-1-61779-965-5

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