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Barcode Sequencing for Understanding Drug–Gene Interactions

  • Andrew M. Smith
  • Tanja Durbic
  • Saranya Kittanakom
  • Guri Giaever
  • Corey NislowEmail author
Part of the Methods in Molecular Biology book series (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.

Key words

Barcode sequencing Multiplexing Bar-seq Pooled competitive growth assays shRNA 

Notes

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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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Andrew M. Smith
    • 1
  • Tanja Durbic
    • 1
  • Saranya Kittanakom
    • 1
  • Guri Giaever
    • 1
  • Corey Nislow
    • 1
    Email author
  1. 1.Donnelly CentreUniversity of TorontoTorontoCanada

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