GEO DataSets

(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) Here we show that deletion of AlgP in mucoid P. aeruginosa strain does not result in nonmucoid phenotype or reduced alginate production. We also show that there is no significant overlap in the AlgP regulon between mucoid and nonmucoid P. aeruginosa strains.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28386

8 Samples

Download data: TXT

(Submitter supplied) The bacterial transcription factor RpoN regulates an extensive network of genes whose products are involved in diverse biological functions. We constructed a small peptide termed the RpoN molecular roadblock, which binds to and blocks transcription from RpoN promoters. This RpoN molecular roadblock can be used in any bacterium to obtain information on the RpoN regulon. We expressed the RpoN molecular roadblock in P. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL84

16 Samples

Download data: CEL

(Submitter supplied) The Pseudomonas aeruginosa response regulator AlgR is critical for the organism's virulence and controls up to 155 different genes. In order to determine which genes are controlled by phosphorylated and unphosphorylated AlgR, phosphomimetic and phosphoablative alleles were recombined onto the chromosome of PAO1. The algR gene was mutated at aspartate 54 to asparagine (D54N) for the phosphoablative allele and mutated at aspartete 54 to glutamate (D54E) for the phosphomimetic allele. more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

9 Samples

Download data: CEL, CHP

(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) The transcriptional regulator AmpR controls expression of the AmpC ß-lactamase in P. aeruginosa and other bacteria. Studies have demonstrated that in addition to regulating ampC expression, AmpR also regulates the expression of the sigma factor AlgT/U and the production of some quorum-sensing regulated virulence factors. In order to understand the ampR regulon, we compared the expression profiles of PAO1 and its isogenic ampR mutant, PAO∆ampR in the presence and absence of sub-MIC ß-lactam stress. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

12 Samples

Download data: CEL

(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) Pseudomonas aeruginosa is an opportunistic pathogen that can adapt to changing environments and can secrete an exopolysaccharide known as alginate as a protection response resulting in a colony morphology and phenotype referred to as mucoid. However how P. aeruginosa senses its environment and activates alginate overproduction is not fully understood. Previously, we showed that Pseudomonas isolation agar (PIA) supplemented with ammonium metavanadate (PIAAMV) induces P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL, CHP

(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

(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) We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17738 GPL17739

12 Samples

Download data: TXT

(Submitter supplied) Pseudomonas aeruginosa uses three type six secretion systems (H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and compete with microbial competitors. These T6SS machines can be loaded with a variety of effectors/toxins, many being associated with a specific VgrG. How P. aeruginosa transcriptionally coordinates the three main T6SS clusters and the multiple vgrG islands spread through the genome is unknown. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

15 Samples

Download data: CSV, XLSX

(Submitter supplied) Representatives of two families of bacterial Par proteins, ParA and ParB, are encoded by the majority of bacterial chromosomes in the close vicinity of oriC. ParA(Soj) and ParB(Spo0J) proteins of Pseudomonas aeruginosa are both important for optimal growth, nucleoids segregation, cell division and different types of motility. Comparative transcriptome analysis of parAnull, parBnull mutants versus parental PAO1161 strain of P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

9 Samples

Download data: CEL

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

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28960 GPL27774

20 Samples

Download data: WIG

(Submitter supplied) We combined phenotypic and genomic assays to provide insight into its role in this pathogen. RpoN was essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping of genome-wide associations of Y. pseudotuberculosis RpoN identified an RpoN-binding motif at 103 inter- and intragenic sites located on both the sense and anti-sense strands Transcriptomic analysis of bacteria lacking rpoN showed a large impact on gene expression, including down-regulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. more...

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28960

12 Samples

Download data: XLSX

(Submitter supplied) We combined phenotypic and genomic assays to provide insight into its role in this pathogen. RpoN was essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping of genome-wide associations of Y. pseudotuberculosis RpoN identified an RpoN-binding motif at 103 inter- and intragenic sites located on both the sense and anti-sense strands. more...

Organism:

Yersinia pseudotuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27774

8 Samples

Download data: WIG, XLSX

(Submitter supplied) RNA-seq analysis of the transcriptome of wild type C.jejuni NCTC11168, and of an rpoN mutant of the same strain, both grown in vitro. ArrayExpress Release Date: 2011-06-14 Publication Title: Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni Publication Author List: Roy R. Chaudhuri, Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell, Andrew J. more...

Organism:

Campylobacter jejuni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13903

4 Samples

Download data

(Submitter supplied) The transcriptome of P. aeruginosa PAO1 in the presence of extracelluar 2-oxoglutarate at a concentration of 20 mM. We determined the transcriptional response of P. aeruignosa PAO1 to extracellular 2-oxoglutarate.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL