GEO DataSets

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

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL3820

53 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to acetate was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL3820

17 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to butanol was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL3820

22 Samples

Download data: GPR

(Submitter supplied) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to butyrate was analyzed. Keywords: stress response

Organism:

Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL3820

14 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of E. coli cells comparing control harboring the empty vector pRadGro (Ec-pR) with E. coli expressing the Deinococcus radiodurans response regulator DR1558 (Ec-1558) Expression of DR1558 conferred to multi-stress tolerance to E. coli.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL20675

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

Type:

Expression profiling by array

Platform:

GPL13359

6 Samples

Download data: TXT

(Submitter supplied) Many reports show an association between the Pst system, the Pho regulon related genes and bacterial virulence. Our previous results showed that a functional Pst system is required for full virulence, resistance to serum, polymyxin B and acid shock. However, the interplay between the Pst system and virulence has an unknown molecular basis. To understand global APEC virulent strain responses to Pho regulon activation, we conducted transcriptome profiling experiments comparing the APEC chi7122 strain and its isogenic Pst mutant grown in rich phosphate medium using the Affymetrix GeneChip® E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL

(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) 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) Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, with a variety of genetic resistance mechanisms previously identified. Using random genomic libraries and DNA microarrays, library inserts were preferentially enriched by culturing in media containing butanol, with successive transfers into fresh media containing incrementally increasing butanol concentrations. more...

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Genome variation profiling by array

Platform:

GPL3820

8 Samples

Download data

(Submitter supplied) Heat-responsive and time-resolved changes in transcriptome of E. coli BL21(DE3) Experimentally mapped transcriptome structure of Escherichia coli BL21(DE3) by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 10 nt).

Organism:

Escherichia coli BL21(DE3)

Type:

Expression profiling by genome tiling array

Platform:

GPL22919

9 Samples

Download data: TXT

(Submitter supplied) Previous evaluation by different molecular and physiological assays of Staphylococcus aureus (S. aureus) responses to heat shock exposure yielded a still fragmentary view of the mechanisms determining bacterial survival or death at supra-physiological temperatures. This study analyzed diverse facets of S. aureus heat-shock adjustment by recording global transcriptomic and metabolic responses of bacterial cultures shifted for 10 min from 37oC to a sub-lethal (43oC) or eventually lethal (48oC) temperature. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL3931

6 Samples

Download data: TXT