GEO DataSets

(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) 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) Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Most CF patients acquire unique P. aeruginosa strains from the environment; however clonal strains have been identified in CF communities in several countries. Two clonal strains infect 10% to 40% of patients in three CF clinics in mainland eastern Australia. The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-2), and four non–clonal CF P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL, CHP

(Submitter supplied) The PANarray design (GPL13324) contains the genes of eight P. aeruginosa genomes in non-redundant format, thus allowing identification of expression of non-PAO1 and other P. aeruginosa genes.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PACS2; Pseudomonas aeruginosa 2192; Pseudomonas aeruginosa LESB58; Pseudomonas aeruginosa AES-1R; Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa C3719; Pseudomonas aeruginosa UCBPP-PA14; Pseudomonas aeruginosa PA7

Type:

Expression profiling by array

Platform:

GPL13324

8 Samples

Download data: TXT

(Submitter supplied) Purpose : The goal of this study was to use RNA Seq to validate transcriptional data of two clinical isolates focussing on a subset of 74 transcript that were selected specifically for Nanostring analysis. Methods : mRNA profiles were generated for the clinical isolates FRD1 and CI224_M, in duplicate, by deep sequencing. Strains were grown for 8 hours in LB medium at 37C prior to RNA harvest. Ribosomal RNA was removed using the Ribi-Zero rRNA Removal Kit (Epicentre). more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

4 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas aeruginosa strains PAHM4 and PAO1 were grown at 37C on LB and RNA was hybridized on the Affymetrix P. aeruginosa chip to compare transcript differences from a BQ isolate to a well characterized wound isolate.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa PAHM4

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL

(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) Pseudomonas aeruginosa evolving in the cystic fibrosis (CF) lung encounters selection via iron-limitation, antibiotics, immune system effectors and other microbes. Standing genetic variation, which depends on rates of horizontal gene transfer (HGT) and mutation supply, controls response to challenges. HGT may increase if new clones successfully invade, while mutator strains increase new mutations. We sought to ascertain genomic signatures of invasion and whether, in the absence of novel invasion, mutator-containing P. aeruginosa populations from chronically infected CF lung are more genetically variable than nonmutator populations. Forty-nine strains from 14 patients treated over three years at Necker Children’s Hospital in Paris were phenotyped for antibiotic resistance, mucoidy and mutator status, and then genotyped by rep-PCR, PFGE and MLST analysis. Overall, strains exhibited greater genetic similarity within patients than among patients, with initial and terminal clones differing markedly between series, indicating unrelated clones independently established infections and resisted invasions that might enlarge genetic variation by sexual recombination. Mutator series were more likely to be multiply antibiotic-resistant, but were no more genetically variable at the single nucleotide level. DNA microarray analyses of bacterial genomes in two longitudinal series of equal duration, one containing and one lacking mutators, revealed both series conspicuously lack genes encoding proteins involved in attachment, motility and amino acid biosynthesis. The mutator series also contained fewer genes hybridizing to canonical PAO1 genome sequences. These data suggest genetic variation arising from mutators may be limited in scope, transient in nature or not easily resolved by fingerprinting, MLST or comparative genomic analyses.

Organism:

Pseudomonas aeruginosa

Type:

Genome variation profiling by array

Platform:

GPL84

10 Samples

Download data: CEL, CHP

(Submitter supplied) Pseudomonas aeruginosa chronically colonizes the lungs of individuals with CF, where it reaches high cell densities and produces a battery of virulence factors. Upon infection, a single strain of P. aeruginosa can colonize an individual’s lungs throughout his or her lifetime. To understand the evolution of P. aeruginosa during chronic lung infection, we conducted both genotypic and phenotypic analyses on clinical isogenic strains obtained from the lungs of three different individuals with CF. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Dataset:

GDS4249

Platform:

GPL84

38 Samples

Download data: CEL

Analysis of clonal isolates collected from three patients with cystic fibrosis (CF). The isolates were collected between 3 months to 8 years after colonization, representing upwards of 39,000 in vivo generations. Results provide insight into the molecular basis of long-term infection of CF lung.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array, transformed count, 4 individual, 19 isolate, 3 other, 4 time sets

Platform:

GPL84

Series:

GSE21966

38 Samples

Download data: CEL

(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) We investigate whether EVs secreted from P. aeruginosa alter MHC antigen expression in lung macrophages, thereby potentially contributing to decreased pathogen clearance.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT

(Submitter supplied) Transcriptional response of P. aeruginosa grown in the presence of 2.5 micromolar testosterone.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

4 Samples

Download data: CSV

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We provide an insight to the DNA auxotrophy of P. aeruginosa PASS4 isolate. Better understanding of P. aeruginosa adaptations in the CF lung environment can have a great impact in the development of specialised treatment regimes aimed at the eradications of P. aeruginosa infections. Methods: P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

12 Samples

Download data: TXT