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Series GSE20305 Query DataSets for GSE20305
Status Public on Feb 13, 2010
Title Time resolved response of E. coli to 5 different stress conditions
Organism Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by array
Summary Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the vast majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here we incorporate the metabolite composition together with gene expression data in order to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared to the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with down regulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.
 
Overall design Four different environmental perturbations, comprising oxidative stress, glucose-lactose diauxic shift, heat, and cold treatments and using an unperturbed culture as a control have been used for transcript profiling. microarray-based transcript profiling was carried out for samples from time points 10-50 min post-perturbation plus two control time points prior to each perturbation for all conditions except the oxidative stress experiment in which all samples (12 time points) were used for transcript profiling covering the entire growth curve, including the stationary phase. Each experimental condition was independently repeated three times.
 
Contributor(s) Jozefczuk S, Steinhauser D, Klie S, Willmitzer L
Citation(s) 20461071
Submission date Feb 12, 2010
Last update date Mar 22, 2012
Contact name Szymon Jozefczuk
E-mail(s) jozefczuk@mpimp-golm.mpg.de
Organization name Max Planck Institute
Street address Am M├╝hlenberg 1
City Potsdam
ZIP/Postal code 14476
Country Germany
 
Platforms (1)
GPL10041 D Steinhauser E.coli 4.4K Agilent Array
Samples (122)
GSM508925 coli_coldstress_timepoint1_rep1
GSM508926 coli_coldstress_timepoint2_rep1
GSM508927 coli_coldstress_timepoint3_rep1
Relations
BioProject PRJNA125345

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
GSE20305_RAW.tar 667.2 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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