GEO DataSets

(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) Geobacter sulfurreducens has a complex metabolism that adapts to use electron acceptors at a wide range of redox potentials. In this study, we used RNA-seq to identify genes associated with electron transfer pathways at different redox potentials. By correlating the RNA-seq data with cyclic voltammetry, we associated several multiheme cytochromes with specific electron transfer pathways.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32116

21 Samples

Download data: CSV, XLSX

(Submitter supplied) We gained insights into the environmental controls of Geobacter activities in cobamide-driven microbiomes by investigating the adaptive responses of the model representative G. sulfurreducens to growth and reproduction in the presence of CoII. Consistent with environmental exposure, we demonstrate high CoII resistance in this species and describe from genomic rand transcriptomic data multiple pathways for protein and DNA repair, cell envelope modifications, and biofilm formation that allow the cells to effectively cope with CoII stress. more...

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29085

4 Samples

Download data: CSV, XLS

(Submitter supplied) Geobacter sulfurreducens is capable of reducing Pd(II) to Pd(0) using pyruvate as an electron donor; however, the biochemical and genetic mechanisms involved in this process have not been described. In this work, we carried out transcriptome profiling analyes to identify genes involved in Pd(II) reduction in this bacteria. Our results showed that 254 genes were upregulated while 142 were downregulated during Pd(II) reduction. more...

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24894

4 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) We applied a ChIP-chip approach to elucidate the binding profiles of sigma factors (RpH, RpoN and RpoS) experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by genome tiling array

Platform:

GPL9112

10 Samples

Download data: PAIR

(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; Expression profiling by high throughput sequencing

Platforms:

GPL9112 GPL10638

29 Samples

Download data: BED, PAIR, WIG

(Submitter supplied) Determine the transcription start sites at 1-bp resolution across the entire G. sulfurreducens genome in multiple growth conditions, including fresh water acetate-fumarate (FWAF) medium, nitrogen limitation and growth on electrode.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10638

3 Samples

Download data: BED, TXT, WIG

(Submitter supplied) We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

Organism:

Geobacter sulfurreducens PCA

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9112

21 Samples

Download data: PAIR

(Submitter supplied) Investigation of comprehensive information about the transcripts (boundary, level, etc.) across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by genome tiling array

Platform:

GPL9112

5 Samples

Download data: PAIR

(Submitter supplied) We applied a ChIP-chip approach to elucidate the σN regulon experimentally under different growth conditions. This technique localizes DNA fragments within σN complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.

Organism:

Geobacter sulfurreducens PCA

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9112

9 Samples

Download data: PAIR

(Submitter supplied) Investigation of comprehensive information about the expression level of RNA transcripts across the entire G.sulfurreducens genome with different nitrogen sources, including NH3, Gln, Asp and N2.

Organism:

Geobacter sulfurreducens PCA

Type:

Expression profiling by genome tiling array

Platform:

GPL9111

12 Samples

Download data: PAIR

(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

Platforms:

GPL9112 GPL9111

21 Samples

Download data: PAIR

(Submitter supplied) Microbially-mediated uranium bioremediation has been demonstrated in uranium contaminated aquifers when acetate was artificially supplied and growth of the natural population of Geobacteraceae was stimulated. In order to mimic the environmental response to acetate, steady-state cells of G. sulfureducens were cultured in chemostats under conditions of either 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor or 2) acetate was supplied in excess with fumarate as sole electron acceptor and limiting factor. more...

Organism:

Geobacter sulfurreducens PCA; Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL5768

22 Samples

Download data: MEV, TAV

(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