Chemical genomic profiling via barcode sequencing to predict compound mode of action

Methods in Molecular Biology

Volumn 1263, Issue , 2015, Pages 299-318

  Piotrowski, Jeff S ^a   Simpkins, Scott W ^a   Li, Sheena C ^a   Deshpande, Raamesh ^a   McIlwain, Sean J ^a   Ong, Irene M ^a   Myers, Chad L ^a   Boone, Charlie ^a   Andersen, Raymond J ^a  

^a NONE

Author keywords

Barcode sequencing; Chemical genomics; Functional genomics; Yeast deletion collection

Indexed keywords

CHEMICAL COMPOUND; GENOMIC DNA;

ARTICLE; CHEMICAL GENOMICS PROFILING; CONTROLLED STUDY; DNA BARCODING; DNA EXTRACTION; GENOME ANALYSIS; GENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; DRUG DEVELOPMENT; DRUG EFFECTS; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PROCEDURES; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

DRUG DISCOVERY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUTATION; SACCHAROMYCES CEREVISIAE;

EID: 84922013769     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2269-7_23     Document Type: Article

References (14)

1. Parsons A et al (2006) Exploring the modeof-action of bioactive compounds by chemicalgenetic profiling in yeast. Cell 126: 611-625
2. Ho CH et al (2011) Combining functional genomics and chemical biology to identify targets of bioactive compounds. Curr Opin Chem Biol 15: 66-78
3. Fung S-Y et al (2013) Unbiased screening of marine sponge extracts for anti-inflammatory agents combined with chemical genomics identifies girolline as an inhibitor of protein synthesis. ACS Chem Biol 9: 247-257
4. Williams DE et al (2011) Padanamides A and B, highly modified linear tetrapeptides produced in culture by a Streptomyces sp. isolated from a marine sediment. Org Lett 13: 3936-3939
5. Giaever G et al (2004) Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A 101: 793-798
6. Giaever G et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391
7. Kim D-U et al (2010) Analysis of a genomewide set of gene deletions in the fission yeast Schizo saccharomyces pombe. Nat Biotechnol 28: 617-623
8. Kitagawa M et al (2006) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 12: 291-299
9. Smith AM et al (2009) Quantitative phenotyping via deep barcode sequencing. Genome Res 19: 1836-1842
10. Costanzo M et al (2010) The genetic landscape of a cell. Science 327: 425-431
11. Robinson DG, Chen W, Storey JD, Gresham D (2014) Design and analysis of bar-seq experiments. G3 (Bethesda) 4: 11-18
12. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140
13. Andrusiak K (2012) Adapting S. cerevisiae chemical genomics for identifying the modes of action of natural compounds. Thesis. https:// tspace. library. utoronto. ca/handle/1807/32456. Accessed 24 Apr 2014
14. Smith AM et al (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38: e142