GEO DataSets

(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) We report the trascriptomic information of wild type (WT) and aceA mutant during the growth on 0.1 % NaAc added MSB media

Organism:

Acinetobacter oleivorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15630

2 Samples

Download data: TXT

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

Type:

Expression profiling by array

Platform:

GPL25406

35 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling in Pseudomonas aeruginosa MPAO1 and its glyoxylate shunt gens transposon insertion mutants (aceA and glcB) was perfomed using microarray analysis with or without 1mM PQ treatment. Based on the gene expression, we investigated role of glyoxylate shunt in P. aeruginosa and found out pathway related with glyoxylate shunt under oxidative stress.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21507

12 Samples

Download data: GPR

(Submitter supplied) Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. more...

Organism:

Acetobacter aceti NBRC 14818

Type:

Expression profiling by array

Platform:

GPL10976

8 Samples

Download data: PAIR

(Submitter supplied) Trascriptome profiles in the cells of A. aceti wild-type strain and its isogenic aceA glcB mutant during growth in medium contaning ethanol and glucose was determined by NimbleGen Eukaryotic Expression array (4x72K).

Organism:

Acetobacter aceti NBRC 14818

Type:

Expression profiling by array

Platform:

GPL10976

4 Samples

Download data: PAIR

(Submitter supplied) Differential gene expression was analyzed between B. japonicum wild type (Bj110) and aceA mutant (BjΔaceA) exposed to desiccation stress to find AceA regulons under the culture condition.

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR

(Submitter supplied) Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate.

Organism:

Pseudonocardia dioxanivorans CB1190

Type:

Expression profiling by array

Platform:

GPL14784

9 Samples

Download data: CEL

(Submitter supplied) MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared Keywords: Growth phase comparison

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL1482

12 Samples

Download data

(Submitter supplied) We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17158

15 Samples

Download data: CSV

(Submitter supplied) Comparision of transcriptome between Burkholderia glumae wild type BGR1 and isocitrate lyase mutant BICL39

Organism:

Burkholderia glumae BGR1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20666

3 Samples

Download data: TXT

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21220 GPL17070

132 Samples

Download data

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

120 Samples

Download data: CSV

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

Platform:

GPL21220

12 Samples

Download data: CSV, GFF

(Submitter supplied) We report that ancestral zinc-finger-domain transcriptional regulators, previously reported to control virulence/symbiosis, implement a cell cycle (S→G1) transcriptional switch. To unravel how this G1-phase transcriptional program is reinstated during a primitive cell cycle, we first defined G1-specific promoters in the model bacterium Caulobacter crescentus by comparative ChIP-Seq analysis. We then exploited one such promoter as genetic proxy, to identify two conserved developmental regulator paralogs, MucR1/2, that constitute a quadripartite and homeostatic regulatory module directing the switch from S→G1-phase transcription. more...

Organism:

Caulobacter vibrioides; Sinorhizobium fredii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18006 GPL18007

11 Samples

Download data: XLS

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

Organism:

Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by array

Platform:

GPL5341

16 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of chemoautotrophically and arabinose supplemented chemoautotrophically grown cells Keywords: Comparison of different lifestyles

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of chemoautotrophically grown cells Keywords: Comparison of different lifestyles

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of arabinose supplemented chemoautotrophically grown cells Keywords: Comparison of different lifestyles

Organism:

Bradyrhizobium diazoefficiens USDA 110; Bradyrhizobium japonicum

Type:

Expression profiling by array

Platform:

GPL5341

6 Samples

Download data: GPR