NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE59408 Query DataSets for GSE59408
Status Public on Sep 17, 2014
Title Prediction of antibiotic resistance by large-scale phenotypic and genotypic data
Organism Escherichia coli
Experiment type Expression profiling by array
Summary The evolution of antibiotic resistance is a clear example of adaptation by natural selection. Although a number of mutations contributing to the resistance have been identified, the relationship between the mutations and the related phenotypic changes responsible for the resistance has yet to be fully elucidated. To better characterize phenotype-genotype mapping for drug resistance, we performed parallel laboratory evolution of Escherichia coli under the selection of single antibiotics and after 90 days propagation obtained resistant strains. We find that an acquisition of resistance to one drug drastically changes the resistance and susceptibility to other drugs. Based on transcriptome data of these strains, we demonstrated that the resistances could be quantitatively predicted by the expression changes of a small number of genes. Whole-genome resequencing analysis provided several candidate mutations contributing to the resistances, while phenotype-genotype mapping was suggested to be complex and included various mutations that caused similar phenotypic changes. The integration of transcriptome and genome data enables us to extract essential phenotypic changes for drug resistances.
 
Overall design To examine the contribution of the gene expression changes to the antibiotic resistances, transcriptome of the parent strain (duplicated) and 40 resistant strains (4 parallel-evolved resistant strains for 10 antibiotics) were analyzed.
 
Contributor(s) Suzuki S, Furusawa C
Citation(s) 25517437
Submission date Jul 14, 2014
Last update date Dec 18, 2014
Contact name Chikara Furusawa
E-mail(s) chikara.furusawa@riken.jp
Organization name RIKEN
Department Quantitative Biology Center (QBiC)
Lab Laboratory for Multiscale Biosystem Dynamics
Street address 6-2-3 Furuedai
City Suita
State/province Osaka
ZIP/Postal code 565-0874
Country Japan
 
Platforms (1)
GPL18948 Agilent-043017 QBiC 8 x 60k E.coli K-12 Expression Ver.1
Samples (42)
GSM1436498 Parent strain_rep1
GSM1436499 Parent strain_rep2
GSM1436500 Cefoperazone (CPZ) resistant strain_Line1
Relations
BioProject PRJNA255254

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE59408_RAW.tar 121.1 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap