GEO DataSets

(Submitter supplied) Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stronger ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

4 Samples

Download data: XLSX

(Submitter supplied) Pleiotropic regulatory mutations affect diverse cellular processes, posing an explicit challenge to our multi-scale understanding of the genotype-phenotype relationships across multiple biological scales. Adaptive Laboratory Evolution (ALE) allows for such mutations to be found and characterized in the context of clear selection pressures. Here, several ALE-selected single-mutation variants in Escherichia coli’s RNA polymerase (RNAP) are detailed using an integrated multi-scale experimental and computational approach. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

10 Samples

Download data: TXT

(Submitter supplied) We report high-throughput RNA sequencing of WT, Δfnr, ΔarcA and Δihf in the exponential phase under anaerobic fermentative conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24659

8 Samples

Download data: TXT

(Submitter supplied) mRNA sequencing was performed on E. coli evolved at 37C on M9 Minimal Media with Glucose

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

11 Samples

Download data: CSV

(Submitter supplied) mRNA sequencing was performed on E. coli evolved at 42C on M9 Minimal Media with Glucose

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

10 Samples

Download data: CSV

(Submitter supplied) Studies of the RNA polymerase-binding molecule ppGpp in bacteria and plants have shown that changes to the kinetics of the RNA polymerase can have dramatic biological effects in the short-term as a stress response. Here we describe the reprogramming of the kinetic parameters of the RNAP through mutations arising during laboratory adaptive evolution of Escherichia coli in minimal media. The mutations cause a 10- to 30-fold decrease in open complex stability at a ribosomal promoter and approximately a 10-fold decrease in transcriptional pausing in the his operon. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(Submitter supplied) RNA Sequencing of wild type Eschrichia coli and a RNA polymerase mutant isolated from deep stationary phase

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

20 Samples

Download data: TXT

(Submitter supplied) Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations could result in large shifts in this fear vs. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26856

38 Samples

Download data: CSV

(Submitter supplied) Time-course gene expression profiles to understand compositional changes of the E. coli K-12 MG1655 transcriptiome during the transition from the exponential growth to the stationary phase

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26856

36 Samples

Download data: CSV

(Submitter supplied) Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26204

9 Samples

Download data: CSV

(Submitter supplied) Cellular tolerance toward ethanol is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to stresses, including ethanol. In order to elucidate the mechanism for enhancement of ethanol tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of ethanol tolerance, we carried out comparative transcriptomic and proteomic analyses with the representative strains E1 and E0 (harboring the ethanol-tolerant mutant E1 of IrrE and the wild type IrrE, respectively). more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(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) Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Genome variation profiling by array

Platform:

GPL4618

19 Samples

Download data: TXT

(Submitter supplied) Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Genome variation profiling by array

Platform:

GPL534

10 Samples

Download data

(Submitter supplied) We report on how the association of mRNA to translating ribosomes changes due to the absence of the expansion segment 27L in S. cerevisiae. We observe specific enrichment and depletion of mRNA sets from rmutant ribosomes which reshapes the proteome.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

12 Samples

Download data: TXT