GEO DataSets

(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) 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) Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Existing experimental data in our lab showed significantly different levels of virulence of "early" and "late" P. aeruginosa infection isolates in a C. elegans slow killing model. We wished to examine the expression profile of these isolates in order to explore genes that may be responsible for the observed differences. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL, CHP

(Submitter supplied) RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) ≤ 0.001, fold change |log2Ratio|≥1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 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) One of the hallmarks of Pseudomonas aeruginosa cystic fibrosis (CF) infection is very high-cell-density (HCD) replication in the lung, allowing this bacterium to induce virulence controlled by HCD quorum-sensing systems. However, the nutrient sources sustaining HCD replication in this chronic infection is largely unknown. Hence, understanding the nutrient factors contributing to HCD in the CF lung will yield new insights into the 'metabolic pathogenicity' and potential treatment of CF infections caused by P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Dataset:

GDS2869

Platform:

GPL84

14 Samples

Download data: CEL, CHP

Analysis of Pseudomonas aeruginosa isolates from sputa of cystic fibrosis (CF) lungs following growth in minimal media. P. aeruginosa infected CF lungs are characterized by high cell density (HCD) replication of this pathogen. Results provide insight into the mechanisms sustaining HCD replication.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array, count, 4 growth protocol, 2 protocol, 3 specimen sets

Platform:

GPL84

Series:

GSE7704

14 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptomic profiles of Pseudomonas protegens H78 and its rpoN-deleted mutant (H78ΔrpoN), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on BGISEQ-500 (illumina).

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24866

6 Samples

Download data: XLS

(Submitter supplied) Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: FASTA, TXT

(Submitter supplied) To gain insights into the initial phases of P. aeruginosa infections and to identify P. aeruginosa genes regulated in response to respiratory epithelia we exposed P. aeruginosa to cultured primary differentiated human airway epithelia. We used a P. aeruginosa strain (PAO1) that causes acute damage to the epithelia and a mutant (PAOSC11) with defects in Type III secretion and in rhamnolipid synthesis. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Dataset:

GDS2502

Platform:

GPL84

8 Samples

Download data

Analysis of Pseudomonas aeruginosa PAO1 or Type III secretion system (TTSS), rhamnolipid synthesis double mutant strain exposed to cultured airway epithelia. TTSS is a virulence factor in acute infections. Strains from chronic infections express decreased levels of TTSS or lack a functional TTSS.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array, count, 2 agent, 2 strain sets

Platform:

GPL84

Series:

GSE4614

8 Samples

Download data

(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) We report the genome-wide effects of blocking the interaction between the sigma-54 bacterial transcriptional enhancer with its cognate promoter in E. coli under nitrogen-starvation conditions.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24672

20 Samples

Download data: TXT

(Submitter supplied) Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in minimal medium with glucose as carbon source (M9G). SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF in Pseudomonas aeruginosa. Deletion of the ECF sigma factor sigX gene provide insights into the SigX role in several virulence and biofilm- related phenotypes in Pseudomonas aeruginosa.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL