GEO DataSets

(Submitter supplied) Previous analysis of gene transcript levels of Geobacter species in groundwater during in situ bioremediation of a uranium-contaminated aquifer detected expression of genes encoding superoxide dismutase (sodA) and cytochrome d ubiquinol oxidase (cydA), proteins known to be involved in the response to oxidative stress in other microorganisms. In order to further elucidate gene expression patterns that could be attributed to oxygen exposure, G. more...

Organism:

Geotalea uraniireducens; Geotalea uraniireducens Rf4

Type:

Expression profiling by array

Platform:

GPL6566

6 Samples

Download data: GPR

(Submitter supplied) Geobacteraceae transfer electrons from a donor such as acetate to an electron acceptor such as Fe(III) or U(VI). Geobacter uraniireducens is found in uranium-contaminated sites and plays an important role in in situ bioremediation. In this experiment, gene expression was compared between G. uraniireducens cultures grown in sediments from a uranium contaminated site amended with acetate and cultures grown in acetate/fumarate medium. more...

Organism:

Geotalea uraniireducens Rf4

Type:

Expression profiling by array

Platform:

GPL6566

6 Samples

Download data: TXT

(Submitter supplied) In the platform data table, the following FEAT_Name values are of controls with additional description: FEAT_NAME Description RCP1_AF168390 A. thaliana root cap 1 protein (RCP1)-Control rbcL_U91966 A. thaliana ribulose-1,5-bisphosphate (rbcL)-control Cab_X56062 A. thaliana chlorophyll a/b-binding protein (Cab)-control rca_M86720 A. thaliana RUBISCO activase (RCA)-control TIM_AF247559 A. thaliana triosephosphate isomerase (TIM)-Control NAC1_AF198054 A. more...

Organism:

Geobacter sulfurreducens PCA

2 Series

33 Samples

Download data: TXT

(Submitter supplied) OmcF is a monoheme c-type cytochrome in Geobacter sulfurreducens. An OmcF-deficient mutant is impaired in iron reduction and electricity production. Heme staining revealed altered expression of several c-type cytochromes in the OmcF-deficient mutant. Whole genome DNA microarray analysis was performed in order to determine which genes demonstrate altered expression in the OmcF-deficient mutant compared to wildtype. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) Geobacter metallireducens serves as the model for Geobacter species that anaerobically oxidize aromatic contaminants with the reduction of Fe(III) oxides in contaminated sediments. Analysis of the complete G. metallireducens genome sequence revealed a 307 kb region, designated the aromatics island, not found in closely related species that do not degrade aromatics. This region encoded enzymes for the degradation of benzoate and other aromatic compounds with the exception of the genes for the conversion of toluene to benzyol-CoA which were in a different region of the genome. more...

Organism:

Geobacter metallireducens GS-15

Type:

Expression profiling by array

Platform:

GPL4028

12 Samples

Download data: TIFF

(Submitter supplied) Microtoming Coupled with Microarray Analysis to Evaluate Potential Differences in the Metabolic Status of Geobacter sulfurreducens at Different Depths in Anode Biofilms Differences in the Metabolic Status of Geobacter sulfurreducens at Different Depths in A Current Producing Biofilm Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL8797

2 Samples

Download data: CEL, CHP

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

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

12 Samples

Download data: GPR

(Submitter supplied) There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were better understood. Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were further understood. Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) Geobacter sulfurreducens was originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate but also to use oxygen as terminal electron acceptor. Research performed has so far only revealed the general ability of G. sulfurreducens to reduce oxygen, but the oxygen consumption rate has not been quantified, nor has evidence been provided as to how the bacterium achieves oxygen consumption. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL26004

12 Samples

Download data: TXT

(Submitter supplied) In this experiment two strains were compared. The control strain was the wild type strain containing the plasmid, pCD341. pCD341 is an inducible expression vector, a plasmid which can be used to make a bacterium produce a protein of interest. It is called inducible, because the protein of interest will only be produced if an inducer, in this case, IPTG, is present. In the control strain pCD341 is "empty", meaning the gene encoding the protein of interest has not been inserted into the vector, so when you add IPTG nothing will be produced. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) Commercial brewing yeast strains are exposed to a number of potential stresses including oxidative stress. The aim of this investigation was to measure the physiological and transcriptional changes of yeast cells during full-scale industrial brewing processes with a view to determining the environmental factors influencing the cell’s oxidative stress response. Cellular antioxidant levels were monitored throughout an industrial propagation and fermentation and microarray analysis was employed to determine transcriptional changes in antioxidant-encoding and other stress response genes. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

17 Samples

Download data: CEL

(Submitter supplied) Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance but research into the mechanisms has been stymied by a lack of a genetically tractable pure culture which unequivocally does not use molecular oxygen to activate benzene. Geobacter metallireducens grew in a medium in which benzene was the sole electron donor and Fe(III) was the sole electron acceptor with a stoichiometry of benzene loss and Fe(III) reduction consistent with benzene oxidation to carbon dioxide coupled with Fe(III) reduction. more...

Organism:

Geobacter metallireducens

Type:

Expression profiling by array

Platform:

GPL14898

15 Samples

Download data: CALLS, PAIR

(Submitter supplied) In this study, expression analysis using electrochemically synthesized Combimatrix 12K DNA microarrays was validated in G sulfurreducens. Growth under nitrogen fixing conditions and growth in ammonium amended medium, respectively, were the experimental and control conditions. Expression analysis using this platform was also compared to expression analysis on whole cDNA microarrays. Keywords: two-condition comparison

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4895

6 Samples

Download data: GPR

(Submitter supplied) The expression profile of adapted G. sulfurreducens strain T9-1 grown with 40 mM fumarate without any other substrate versus the expression profile of G. sulfurreducens PCA (wild type) grown with 10 mM acetate and 40 mM fumarate

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30660

6 Samples

Download data: TXT

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

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9112

16 Samples

Download data: GFF, PAIR

(Submitter supplied) Fur is a transcriptional regulator whose activity is dependent on Fe(II) concentrations. Chromatin immunoprecipitation (ChIP) coupled to microarray analysis allowed for the identification of Fur binding sites within the G. sulfurreducens genome.

Organism:

Geobacter sulfurreducens PCA

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9112

7 Samples

Download data: GFF, PAIR

(Submitter supplied) G. sulfurreducens was cultured on a variety of different iron concentrations and differential expression analysis was used to identify the iron stimulon.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by genome tiling array

Platform:

GPL9112

9 Samples

Download data: GFF, PAIR

(Submitter supplied) Previous studies demonstrated that an outer membrane c-type cytochrome, OmcB (GSU_2737), was involved in Fe(III) reduction in Geobacter sulfurreducens. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing omcB restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). more...

Organism:

Geobacter sulfurreducens; Geobacter sulfurreducens PCA

Type:

Expression profiling by array

Platform:

GPL5768

11 Samples

Download data: TAV

(Submitter supplied) We report the differential expression of a PAH degrading bacterium in different states of substrate induction.

Organism:

Mycolicibacterium gilvum PYR-GCK

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16708

2 Samples

Download data: XLSX