GEO DataSets

(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) 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) The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alpha-proteobacteria. Based on the complete Rhizobium etli genome sequence, we constructed the R. etli CFN42 oligonucleotide (70 mer) microarray, and utilized this tool to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain in symbiosis with Phaseolus vulgaris. As expected, the genes associated with a NifA and RpoN binding sites were downregulated in the NifA mutant strain.

Organism:

Rhizobium etli CFN 42

Type:

Expression profiling by array

Platform:

GPL10081

3 Samples

Download data: TXT

(Submitter supplied) DNA microarray technology was used to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain under microaerobic (free living) conditions. As expected, several genes associated with a NifA binding site were downregulated in the NifA mutant strain.

Organism:

Rhizobium etli CFN 42

Type:

Expression profiling by array

Platform:

GPL10081

3 Samples

Download data

(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) G. sulfurreducens can generate electricity from the oxidation of organic compounds. This is because it can take electrons from organic compounds and ship them out to the outer surface of the cell where they can then be deposited on various insoluble electron acceptors including electrodes. Cells attatched to the surface of an electrode oxidize acetate and and deposit the electrons derived from acetate onto the surface of the electrode after which they can travel through an electrical circuit, producing a current. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σD and σN. Among the seven σ factors in Escherichia coli, six belongs to the σD family. Each σ factor recognizes a group of promoters, providing effective control of differential gene expression. Many studies have shown that σ factors of the σD family compete with each other for function. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL3154

9 Samples

Download data: CEL, CHP

(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) Integration host factor (IHF) is a widely distributed small heterodimeric protein member of the bacterial Nucleoid-Associated Proteins (NAPs), implicated in multiple DNA regulatory process. IHF recognizes a specific DNA sequence and induces a large bend of the nucleic acid. IHF function has been mainly linked with regulation of s54-dependent promoters, where IHF commonly recognizes a DNA sequence between the enhancer-binding region and the promoter, facilitating a close contact between the upstream bound activator and the promoter bound, RNA polymerase. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29367

6 Samples

Download data: TXT

(Submitter supplied) Alginate overproduction by P. aeruginosa, also known as mucoidy is associated with chronic endobronchial infections in cystic fibrosis (CF). Alginate biosynthesis in this bacterium is initiated by the extracytoplasmic function sigma factor (σ22, AlgU/T). In the wild type (wt) nonmucoid strains, such as PAO1, AlgU is sequestered by the anti-sigma factor MucA that inhibits alginate production. However, the degradation of MucA by activated intramembrane proteases AlgW and/or MucP can lead to the conversion from nonmucoid strains to mucoid. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Dataset:

GDS4254

Platform:

GPL84

6 Samples

Download data: CEL, CHP

Analysis of Pseudomonas aeruginosa PAO1 mucoid kinB mutant and nonmucoid kinB rpoN double mutant. Deletion of the sensor kinase KinB results in alginate overproduction, a trait associated with chronic endobronchial infections in cystic fibrosis. Sigma Factor RpoN is required for mucoid induction.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL84

Series:

GSE35248

6 Samples

Download data: CEL, CHP

(Submitter supplied) There is increasing evidence to support a role for sigma factor 54 (RpoN) in the regulation of stress resistance factors and protein secretion systems important to bacterial transmission and pathogenesis. In enterohemorrhagic E. coli O157:H7, acid resistance and type III secretion are essential determinants of gastric passage and colonization. This study thus described the transcriptome of an rpoN null strain of E. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL7445

8 Samples

Download data: GPR

(Submitter supplied) The phytopathogen Xylella fastidiosa produces two classes of pili, long type IV pili and short type I pili, which are involved in motility and adhesion. In this work, we have investigated the role of σ54 factor and its involvement in the regulation of fimbrial biogenesis in X. fastidiosa. An rpoN null mutant was constructed from citrus strain J1a12, and analyses of global gene expression profile by microarrays comparing the wild type and rpoN mutant strains showed that few genes exhibited differential expression. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

6 Samples

Download data

(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 PCA; Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL5768

11 Samples

Download data: TAV

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

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4895

12 Samples

Download data: GPR, TXT

(Submitter supplied) Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4895

6 Samples

Download data: GPR, TXT

(Submitter supplied) Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4895

6 Samples

Download data: GPR, TXT

(Submitter supplied) Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. more...

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL6368

10 Samples

Download data