GEO DataSets

(Submitter supplied) The goal of this study is to explore genes that are differentially expressed in E. coli C strains (wt and a butanol-tolerant mutant) after 1-butanol treatment. The butanol-tolerant mutant strain PKH5000 (denoted by 'E' for 'evolved') were derived from KCTC 2571 (wt) (denoted by 'A' for 'ancestral') by proton beam irradiation. 0 and 1 in sample title mean before and after butanol treatment, respectively.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL7395

18 Samples

Download data: GPR

(Submitter supplied) Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli. The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent)

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL8984

16 Samples

Download data: GPR

(Submitter supplied) We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.

Organism:

Escherichia coli CFT073; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL13359

6 Samples

Download data: TXT

(Submitter supplied) Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance. The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT. Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL8984

24 Samples

Download data: GPR

(Submitter supplied) Exogenous isopentenol was added to a culture of E. coli and the RNA expression response was measured using Nimblegen arrays. Genes highly upregulated were then subsequently overexpressed to improve the tolerance to isopentenol toxicity. In addition a subset of genes that improved the tolerance were also overexpressed in a producing strain, leading to improved production over the empty vector control. more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL14649

6 Samples

Download data: PAIR

(Submitter supplied) Isobutanol has emerged as a potential biofuel due to recent metabolic engineering efforts. Here we used gene expression and transcription factor(TF)-gene interaction data, genetic knockouts, and Network Component Analysis (NCA) to map the isobutanol response network of Escherichia coli under aerobic conditions. A transcriptional response network consisting of 2004 genes/TFs and 2600 interactions was identified. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL5113

66 Samples

Download data

(Submitter supplied) n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL8811

12 Samples

Download data: TXT

(Submitter supplied) Although the relationship between phenotypic plasticity and evolutionary dynamics has attracted large interest, very little is known about the contribution of phenotypic plasticity to adaptive evolution. In this study, we analyzed phenotypic and genotypic changes in E. coli cells during adaptive evolution to ethanol stress. To quantify the phenotypic changes, transcriptome analyses were performed.

Organism:

Escherichia coli

Type:

Expression profiling by genome tiling array

Platform:

GPL13336

31 Samples

Download data: CEL, TXT

(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) To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18948

8 Samples

Download data: TXT

(Submitter supplied) Butanol is a bulk chemical feedstock and a promising fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Transcript regulator factor Rob plays an important role in butanol-tolerant functional revealed by our previous study. In this study, the mutant strain DTrob (AT686-687 deletion in rob gene) could tolerate 1.25 %(v/v) butanol. And the per unit intracellular butanol concentration and transcriptome of wild-type and DTrob were further compared to understand the regulation mechanism of Rob for butanol tolerance. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

2 Samples

Download data: TXT, XLSX

(Submitter supplied) The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. more...

Organism:

Levilactobacillus brevis

Type:

Expression profiling by array

Platform:

GPL10674

21 Samples

Download data: GPR

(Submitter supplied) Microbes exhibit short and long term responses when exposed to challenging environmental conditions. To what extent these responses are correlated, what their evolutionary potential is and how they translate to cross-stress fitness is still unclear. In this study, we comprehensively characterized the response of Escherichia coli populations to four abiotic stresses (n-butanol, osmotic, acidic, and oxidative) and their combinations by performing genome-scale transcriptional analysis and growth profiling. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

40 Samples

Download data: FPKM_TRACKING

(Submitter supplied) The goal of this experiment is to identify the pathways that are deregulated as part of an adaptive response to high levels of ethanol in the media.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL10286

2 Samples

Download data: TXT

(Submitter supplied) Here we applied adaptive laboratory evolution successfully to evolve E. coli towards high tolerance against isoprenol, increasing growth at the half-maximal inhibitory concentration by 47%. RNA-sequencing showed that the deletion identified upstream of yghB correlated with a strong overexpression of the gene.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29216

12 Samples

Download data: CSV

(Submitter supplied) We use adaptive laboratory evolution to generate strains which tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulon analysis of the transcripome, and metabolic models to elucidate six interacting stress tolerance mechanisms: 1) modification of transport, 2) activation of ROS stress responses, 3) use of ROS-sensitive iron regulation, 4) motility, 5) broad transcriptional reallocation toward growth, and 6) metabolic rewiring to decrease NADH production. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24659

84 Samples

Download data: CSV

(Submitter supplied) E. coli frequently encounters oxidative stress both in its natural environment or in industrial biotechnology. Elucidating the mechanisms behind tolerance to oxidative stress would be beneficial for understanding pathogenesis as well as improving production strain fitness. We make use of adaptive laboratory evolution to develop two strains of E. coli which exhibit 500% increased tolerance to paraquat stress compared to wild type. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

22 Samples

Download data: CSV, TXT