GEO DataSets

(Submitter supplied) Scaling up the functioning of synthetic circuits from microplates to bioreactors is far from trivial to achieve. We here test the scalability performance of a previously developed growth switch for increasing product yields in bacteria, based on external control of RNA polymerase expression. We show that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25140

18 Samples

Download data: CSV, TXT

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

Organism:

Escherichia coli

Type:

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

Platforms:

GPL28126 GPL29469 GPL21433

14 Samples

Download data: GFF, HTML, TXT

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we found spontaneous mutations in the conserved regions of AC and CRP.

Organism:

Escherichia coli

Type:

Other

Platform:

GPL29469

3 Samples

Download data: HTML, TXT

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

6 Samples

Download data: GFF

(Submitter supplied) Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28126

5 Samples

Download data: GFF

(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) 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) M9 glucose minimum media were analyzed for RNA expression. We use this expression information to show that mRNA level correlate with codon efficiency (Boel et al., Nature 2015)

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

1 Sample

Download data: CEL, CHP

(Submitter supplied) We measured transcriptional changes in an effort to understand mechanisms of action resulting from the introduction of global transcriptional machinery engineering in E. coli in the presence and absence of ethanol. Keywords: repeat

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

20 Samples

Download data: CEL