GEO DataSets

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

9 Samples

Download data: PAIR

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

35 Samples

Download data: PAIR

(Submitter supplied) Translational regulation was investigated at the genome scale in Escherichia coli cells. Using the polysome profiling method, the ribosome occupancy (RO) and ribosome density (RD) of different mRNA copies were determined for several hundred mRNAs during the exponential and stationary phases, providing the most complete characterisation of such regulation in E. coli. Although for most genes, nearly all mRNAs (>90%) were undergoing translation, they were loaded with far fewer than the theoretical maximum number of ribosomes, suggesting translation limitation at the initiation step. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21726

42 Samples

Download data: CSV

(Submitter supplied) The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. more...

Organism:

Caulobacter vibrioides CB15; Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL10469

8 Samples

Download data: TXT

(Submitter supplied) How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

36 Samples

Download data: CSV

(Submitter supplied) Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL4995

136 Samples

Download data: TXT

(Submitter supplied) nylon membranes positively charged 8*12 cm Protocol: Amplicons (PCR) were designed and amplified by Eurogentec. A mean length of 535 bp and final concentrations between 40 and 380 µg/l were obtained. PCR were diluted in DMSO 50 % in 384 wells spot plates and spotted (4 deposits/ spot) in duplicate on positively charged nylon membranes (Roche) with a Biogrid spotter (Biorobotics) with a 4*4 pattern.

Organism:

Lactococcus lactis

3 Series

30 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) Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) In bacterial adaptation to the dynamic environment, metabolic genes are typically thought to be the executors, whereas global transcription regulators are regarded as the decision makers. Although the feedback from metabolic consequence is believed to be important, much less is understood. This work demonstrates that the gluconeogenic genes in Escherichia coli, ppsA, sfcA, and maeB, provide a feedback loop to the global regulator, CRP, in carbon source transition. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

4 related Platforms

81 Samples

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(Submitter supplied) Our laboratory has recently discovered that E. coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for Thymineless Death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses on actively growing optA1 gpt strains subjected to hypoxanthine deprivation for increasing periods of time. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3154

90 Samples

Download data: CEL, CHP

(Submitter supplied) Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

24 Samples

Download data: TXT

(Submitter supplied) We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the carbon monoxide releasing molecule, CORM-2. The E. coli microarray analysis shows that E. coli CORM-2 response is multifaceted with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in posttranslational modification, such as chaperones. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL, CHP

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

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL3820

53 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to acetate was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL3820

17 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to butanol was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL3820

22 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to butyrate was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL3820

14 Samples

Download data: GPR

(Submitter supplied) Adaptation of Lactococcus lactis towards progressive carbon starvation is mediated by three different types of transcriptomic responses: i) global responses, i.e. general decrease of functions linked to bacterial growth and lack of induction of the general stress response, ii) specific responses functionally related to glucose exhaustion, i.e. under expression of central metabolism genes, induction of alternative sugars transport and metabolism genes, induction of arginine deiminase pathway genes and iii) other responses never described previously during carbon starvation. more...

Organism:

Lactococcus lactis

Type:

Expression profiling by array

Platform:

GPL3782

12 Samples

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(Submitter supplied) We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. Quantitative coarse-grained expression-pattern analysis demonstrated that the gene expression trend following immediately the reduction of carbon influx flow rate was determined by its initial expression level. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

24 Samples

Download data: TXT

(Submitter supplied) We use RNA-seq and Ribo-seq to analyze expression changes in the Long Term Evolution Experiment. By comparing expression levels between the ancestral strains and each of the evolved lines, we find that expression changes are largely parallel after 22 years of evolution, that these changes occur in specific pathways, and that known mutations may be responsible for some of the observed expression changes.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21222

8 Samples

Download data: CSV, TSV