GEO DataSets

Analysis of anaerobic steady-state cultures at various time points up to 1 hour following perturbation by introduction of air. Results provide insight into the molecular dynamics underlying the adaptation to aerobic growth.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, log2 ratio, 4 time sets

Platform:

GPL534

Series:

GSE4735

4 Samples

Download data: TXT

(Submitter supplied) Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Several previous transcript-profiling experiments have compared separate anaerobic and aerobic cultures. Here, for the first time, the process of adaptation was investigated by determining changes in transcript profiles when anaerobic steady-state cultures were perturbed by the introduction of air. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS2364

Platform:

GPL534

4 Samples

Download data: TXT

(Submitter supplied) Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Here, the process of adaptation was investigated by determining changes in transcript profiles when aerobic steady-state cultures were depleted of air. Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 300 rpm and the temperature maintained at 37 °C. more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

Download data: TXT

(Submitter supplied) E. coli K12 strain W3110 was used in this study. Cells were grown anaerobically in defined medium at pH7 and 37°C in a stirred 3-liter bioreactor until the culture reached an OD (600nm) of 3. At that point the first sample was drawn and aeration was started subsequently at 1l/min. 0.5, 1, 2, 5, and 10 min after the onset of aeration additional samples were drawn.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

18 Samples

Download data: XLSX

(Submitter supplied) Escherichia coli strains MG1655 and an isogenic hmp::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions.. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

20 Samples

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(Submitter supplied) Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 8 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) This study examined the genes under the control of FlhDC and sigmaF in E. coli. Keywords: wild-type, deletion and overexepression strains

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

15 Samples

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(Submitter supplied) A total of 4388/4385 genes' transcripts (under aerobic/microaerobic condition, respectively) were identified. Among them, 105 and 71 transcripts were confidently determined to be up- or down-regulated by more than 4 folds with false discovery rate (FDR) p value more than 1, respectively. Additionally, 49 known regulatory non-coding small RNAs (sRNAs) were detected, and 18 sRNAs were differentially abundant (more than 1.5 fold-change). more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL16085

15 Samples

Download data: XLSX

(Submitter supplied) Cytochrome oxydases and quinol monooxygenase were removed from the E. coli genome resulting in oxygen-independent physiology We used microarray profiling to identify perturbed metabolic or regulatory functionality resulting in the inability to undergo aerobic-anaerobic shift.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(Submitter supplied) Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

4 Samples

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(Submitter supplied) Small RNAs (sRNA) that act by base pairing with trans-encoded mRNAs modulate metabolism in response to a variety of environmental stimuli. Here, we describe an Hfq-binding sRNA (FnrS) whose expression is induced upon a shift from aerobic to anaerobic conditions and which acts to down regulate the levels of a variety of mRNAs encoding metabolic enzymes. Anaerobic induction in minimal medium depends strongly on FNR but is also affected by ArcA and CRP. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL, CHP

(Submitter supplied) To study the dynamics of acid adaptation in E.coli Keio collection mutant library at pH7 and pH5.5 after 15 minutes of adaptation Keywords: Single channel hybridisation were carried out using cy5 dye.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7535

62 Samples

Download data: CSV

(Submitter supplied) To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

8 Samples

Download data: TXT