Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of P. aeruginosa isolated from 3 individuals with cystic fibrosis over time

ABSTRACT: 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 individualâs 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. These strains were isolated over a period of approximately ten years and possess phenotypes that are commonly observed in isolates from the CF lung, such as the antibiotic resistant dwarf and mucoid phenotypes. Microarray analyses were carried out on isolates grown in a chemically defined medium that mimics the nutritional environment of the CF lung, synthetic CF sputum medium (SCFM). 17 clinically isolated P. aeruginosa strains from three individuals with CF (5 strains from individual P1, 7 strains from individual P2, 5 strains from individual P3). Two reference strains PAO1 and PA14. All experiments were biologically duplicated.

ORGANISM(S): Pseudomonas aeruginosa

SUBMITTER: Holly Huse

PROVIDER: E-GEOD-21966 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Microarray analysis of P. aeruginosa PAO1 expression PA5060 (phaF) on pJN105

Project description:The Pseudomonas aeruginosa PAO1 gene phaF (PA5060) is a transcriptional regulator in the closely related pseudomonad P. putida. phaF is expressed at higher levels in P. aeruginosa clinical isolates from the cystic fibrosis respiratory tract. To determine the role of phaF in regulating P. aeruginosa gene expression, we cloned it under control of the pBAD promoter in expression vector pJN105 and compared expression in this strain relative to an empty vector control strain. We used microarrays to study overall gene expression in a P. aeruginosa PAO1 phaF overexpression strain. A P. aeruginosa PAO1 strain over-expressing the transcriptional regulator phaF, PAO1 pJN105-phaF, and the corresponding empty control strain, P. aeruginosa PAO1 pJN105, were grown to exponential phase, RNA was isolated, and gene expression was analyzed via microarray analysis and compared.

2013-06-21 | E-GEOD-47173 | biostudies-arrayexpress

Transcriptional profiling of P. aeruginosa isolated from 3 individuals with cystic fibrosis over time

Project description: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. These strains were isolated over a period of approximately ten years and possess phenotypes that are commonly observed in isolates from the CF lung, such as the antibiotic resistant dwarf and mucoid phenotypes. Microarray analyses were carried out on isolates grown in a chemically defined medium that mimics the nutritional environment of the CF lung, synthetic CF sputum medium (SCFM).

2010-05-25 | GSE21966 | GEO

Pseudomonas aeruginosa cystic fibrosis strains share a core proteome

Project description:The opportunistic pathogen Pseudomonas aeruginosa is among the main colonizers of the lungs of cystic fibrosis (CF) patients. We have isolated and sequenced several P. aeruginosa isolates from the sputum of CF patients and used phenotypic, genomic and proteomic analyses to compare these CF derived strains with each other and with the model strain PAO1.

2015-10-14 | PXD002865 | Pride

Analysis of Pseudomonas aeruginosa evolving in the cystic fibrosis lung uncovers limited evidence that mutator lineages are more genetically variable than non-mutator lineages

Project description: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. Clinical P. aeruginosa hypermutator and nonhypermutator lineages from CF lung. Array-based genome hybridization.

2011-10-31 | E-GEOD-25481 | biostudies-arrayexpress

Gene expression in AES-2 clonal isolates of Pseudomonas aeruginosa

Project description: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. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization

2009-02-05 | GSE10304 | GEO

Gene expression in PAO1, clonal AES-1 and non-clonal isolates of Pseudomonas aeruginosa

Project description: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-1), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization

2008-12-05 | GSE6122 | GEO

Gene expression data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections

Project description:Pseudomonas aeruginosa is a common pathogen in the lungs of the cystic fibrosis patients. As infection develops the organism progressively adapts to its environment and its mode of pathogenesis alters, frequently including the loss of quorum sensing regulated virulence factors. We used microarrays to detail differences between two P. aeruginosa isolates from CF patients, one of which (UUPA38) exhibited an active quorum sensing system (QS+) typical of early acute infection while the other (UUPA85) was QS-compromised (QS-) typical of chronic CF-adapted infection. Bacterial cell biomass was harvested from triplicate biofilm and planktonic cultures of each of 2 strains of P. aeruginosa. RNA was extracted, converted to cDNA and hybridized to Affymetrix microarrays. We aimed to identify genes which were differentially transcribed between the 2 isolates during both modes of growth.

2010-11-04 | E-GEOD-25128 | biostudies-arrayexpress

Transcription profiling of Pseudomonas aeruginosa wild type and transcriptional regulator pycR isogenic mutants

Project description:Evaluate role of the transcriptional regulator PycR in regulation of Pseudomonas aeruginosa virulence gene expression

2008-05-07 | E-MEXP-1591 | biostudies-arrayexpress

Expression data of Pseudomonas aeruginosa isolates from Cystic Fibrosis patients in Denmark

Project description:CF patients suffer from chronic and recurrent respiratory tract infections which eventually lead to lung failure followed by death. Pseudomonas aeruginosa is one of the major pathogens for CF patients and is the principal cause of mortality and morbidity in CF patients. Once it gets adapted, P. aeruginosa can persist for several decades in the respiratory tracts of CF patients, overcoming host defense mechanisms as well as intensive antibiotic therapies. P. aeruginosa CF strains isolated from different infection stage were selected for RNA extraction and hybridization on Affymetrix microarrays. Two batch of P. aeruginosa CF isolates are chosen : 1) isolates from a group of patients since 1973-2008 as described in ref (PMID: 21518885); 2) isolates from a group of newly infected children as described in ref (PMID: 20406284).

2011-08-05 | E-GEOD-31227 | biostudies-arrayexpress

Novel virulence factors in host-adapted Pseudomonas aeruginosa infection of the Cystic Fibrosis airways

Project description:Pseudomonas aeruginosa airway infection is the primary cause of death in Cystic Fibrosis (CF). During early infection P. aeruginosa produces multiple virulence factors, which cause acute pulmonary disease and are largely regulated by quorum sensing (QS) intercellular signalling networks. Longitudinal clinical studies have observed the loss, through adaptive mutation, of QS and QS-related virulence in late chronic infection. Although the mechanisms are not understood, infection with QS mutants has been linked to a worse outcome for CF patients. By comparing QS-active and QS-inactive P. aeruginosa CF isolates, we have identified novel virulence factors and pathways associated with QS disruption. In particular, we noted factors implicating increased intra-phagocyte survival. Our data present novel targets as candidates for future CF therapies. Some of these targets are already the subject of drug development programmes for the treatment of other bacterial pathogens and may provide cross-over benefit to the CF population. Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE25128: Gene expression data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections GSE25129: Comparative genomic hybridisation data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections

2010-11-04 | E-GEOD-25130 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data