title: Barcode sequencing for understanding drug-gene interactions.
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.
authors: Donnelly Centre, University of Toronto, Toronto, ON, Canada.
authors: Andrew M
authors: AM
authors: Smith
authors: Tanja
authors: T
authors: Durbic
authors: Saranya
authors: S
authors: Kittanakom
authors: Guri
authors: G
authors: Giaever
authors: Corey
authors: C
authors: Nislow
mesh_terms: D000818:Animals; D017353:Gene Deletion; D055786:Gene Knockout Techniques; D005796:Genes / Q000235:genetics*; D006801:Humans; D009154:Mutation; D004364:Pharmaceutical Preparations / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004364:Pharmaceutical Preparations; D034741:RNA, Small Interfering