GEO DataSets

(Submitter supplied) This study was conducted to determine the impact of extreme temperatures, aiming at controlling microorganisms by cooking, on the physiology and the transcriptome of Escherichia coli. ABSTRACT: Because the genome of Escherichia coli K12 is well understood, this organism was used as a model to investigate physiological and molecular changes during cell adaptation and survival to cooking temperatures used in the food industry. more...

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13360

18 Samples

Download data: TXT

(Submitter supplied) Because many virulence genes in E. coli and other pathogens are regulated by temperature, we wanted to determine on a genome-wide scale which genes are modulated in adapting to both human host temperature (37˚C) and ambient room temperature (23˚C). Overall, 126 genes were found to be more highly expressed at 37˚C (1) whereas 297 genes were more highly expressed at 23˚C (2). Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the 37˚C list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL5942

5 Samples

Download data: GPR, TXT

(Submitter supplied) We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

18 Samples

Download data: CEL, CHP

(Submitter supplied) Survival of the foodborne pathogen Listeria monocytogenes in acidic environments (e.g., stomach and low pH foods) is vital to its transmission. L. monocytogenes grows at temperatures as low as 2°C, and refrigerated, ready-to-eat foods have been sources of L. monocytogenes outbreaks. The purpose of this study was to determine whether growth at a low temperature (i.e., 7°C) affects the response of L. monocytogenes to sudden acid shock.

Organism:

Listeria innocua; Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL5029

10 Samples

Download data: GPR

(Submitter supplied) mRNA sequencing was performed on E. coli evolved at 42C on M9 Minimal Media with Glucose

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

10 Samples

Download data: CSV

(Submitter supplied) Microarray consists of full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli mg1655 (1). PCR products are printed in replicate on standard, 1” X 3”, poly-l-lysine coated glass microscope slides. Greater than 95% have been shown to migrate as a single band, of the predicted molecular weight, as determined by gel electrophoresis and ethidium bromide staining. Also printed on each microarray are >200 control spots consisting of: fragmented E. more...

Organism:

Escherichia coli

1 Series

5 Samples

Download data: TXT

(Submitter supplied) The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL6272

12 Samples

Download data: TXT

(Submitter supplied) Previous evaluation by different molecular and physiological assays of Staphylococcus aureus (S. aureus) responses to heat shock exposure yielded a still fragmentary view of the mechanisms determining bacterial survival or death at supra-physiological temperatures. This study analyzed diverse facets of S. aureus heat-shock adjustment by recording global transcriptomic and metabolic responses of bacterial cultures shifted for 10 min from 37oC to a sub-lethal (43oC) or eventually lethal (48oC) temperature. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL3931

6 Samples

Download data: TXT

(Submitter supplied) Metals at high concentrations can exert toxic effects on microorganisms. It has been widely reported that lowering environmental pH reduces effects of cadmium toxicity in bacteria. Understanding the effects of pH-mediated cadmium toxicity on bacteria would be useful for minimizing cadmium toxicity in the environment and gaining insight into the interactions between organic and inorganic components of life. more...

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL6540

8 Samples

Download data: MEV

(Submitter supplied) This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli. In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) This study explores the effects of glycerol, on whole genome expression of Escherichia coli. DNA microarray analysis imply that E. coli in the presence of glycerol generates acidic metabolites to which it adapts by upregulation of genes involved in acid stress and by simultaneously downregulating genes involved in high pH stress.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(Submitter supplied) We varied RpoS levels using a mutation or an arabinose-inducible RpoS construct during stationary phase in rich media. We then sequenced cDNA from three separate RpoS levels, corresponding to 0%, 26% and 100% of wild-type levels.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: GFF, TXT

(Submitter supplied) Microarray hybridization of cDNA libraries obtained from exponentially growing or heat-shocked AW1.7 or GGG10 cultures was performed to compare gene expression of these two strains. Expression of selected genes from different functional groups was quantified by quantitative PCR (q-PCR). DnaK, 30S and 50S risobomal subunits were overexpressed in E. coli GGG10 relative to E. coli AW1.7 upon heat shock at 50°C, indicating improved ribosome stability. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL13208

6 Samples

Download data: TXT

(Submitter supplied) As the foodborne pathogen Listeria monocytogenes has the ability to grow at refrigeration temperatures, whole-genome microarray experiments were performed using L. monocytogenes strain 10403S to define the cold stress regulon and to identify genes differentially expressed during growth at 4°C and 37°C. Microarray analysis using a stringent cutoff (adjusted p<0.001; fold-change >2.0) revealed 105 and 170 genes that showed higher transcript levels in logarithmic- and stationary-phase cells, respectively, at 4°C (compared to cells at 37°C). more...

Organism:

Listeria monocytogenes; Listeria innocua

Type:

Expression profiling by array

Platform:

GPL5029

2 Samples

Download data: GPR