GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE110137 Query DataSets for GSE110137
Status Public on Mar 25, 2019
Title Mode of action characterization of antibiotics using expression profile fingerprints generated by RNA-sequencing technology
Organism Escherichia coli BW25113
Experiment type Expression profiling by high throughput sequencing
Summary RNA-seq based transcriptome profiling allows a detailed molecular analysis of the E.coli transcriptome (~4200 genes) after perturbation with different antibiotics. Transcriptome fingerprints enable the identification of gene and pathway level responses to treatment to derive a mechanistic understanding of antibiotics mode of action and to differentiate antibiotics. For this goal, treatment has to be performed in a short time period and with sublethal concentrations of the antibiotics. Sublethal concentrations were chosen based on the EC90 concentration of the antibiotic necessary to change the cellular morphology compared to control conditions.
Conclusions: Our study represents the first detailed analysis of E.coli transcriptomes after treatment with different antibiotics, with biologic replicates, generated by RNA-seq technology. The experimental design and data analysis reported here should provide a framework for comparative investigations of expression profiles of known and novel antibiotics. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Overall design mRNA profiles of E.coli treated with different antibiotics at sublethal concentration and measured by deep RNA-sequencing, in triplicate, using Illumina HiSeq2500
Contributor(s) Heckel T, Clausen I, Schmucki R, Prunotto M, Jensen Zoffmann S
Citation(s) 30899034
Submission date Feb 05, 2018
Last update date Mar 27, 2019
Contact name Roland Schmucki
Organization name F. Hoffmann - La Roche AG
Street address Grenzacherstrase
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL20227 Illumina HiSeq 2500 (Escherichia coli BW25113)
Samples (57)
GSM2978339 PDD_P2_18
GSM2978340 PDD_P2_44
GSM2978341 PDD_P2_70
BioProject PRJNA432937
SRA SRP132189

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
GSE110137_counts.gct.gz 760.5 Kb (ftp)(http) GCT
GSE110137_rpkms.gct.gz 622.8 Kb (ftp)(http) GCT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap