GEO DataSets

(Submitter supplied) To understand the gene response during the glucose to acetate diauxic transition, we grew E. coli in minimal media with acetate and a small amount of glucose. Cells were collected and RNA was purified at different time points during the growth transition, including pre-shift (growth on glucose), 5 minutes, 15 minutes, 60 minutes and 120 minutes after glucose run-out, and steady state growth on acetate (post-shift).

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24377

6 Samples

Download data: TXT

(Submitter supplied) Escherichia coli was evolved under growth conditions in which the carbon substrate alternated between glucose and either glycerol, xylose, or acetate with every tube of growth. Controls were also evolved to each substrate individually, without switching.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

23 Samples

Download data: TXT

(Submitter supplied) Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.

Organism:

Escherichia coli K-12

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26204

30 Samples

Download data: XLSX

(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

(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

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) The global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions.  Lrp has previously been shown to activate or repress approximately 10% of genes in Escherichia coli.  However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study.  We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21222

108 Samples

Download data: TSV

(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) Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

96 Samples

Download data: CEL

(Submitter supplied) Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogenous environment. During this incubation, E. coli acquires mutations that are selected for in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

4 Samples

Download data: TXT