PAHM4 vs PAO1 37C LB
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa PAHM4
SUBMITTER: John Varga
PROVIDER: E-GEOD-40461 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Pseudomonas aeruginosa strain PAO1 was grown at 22M-BM-0C and 37M-BM-0C in Lysogeny broth (LB) and RNA was hybridized on the Affymetrix P. aeruginosa chip. PAO1 was grown in triplicate in Lysogeny broth at 22M-BM-0C or 37M-BM-0C. Total RNA from each sample was pooled and amplified then assayed in triplicate resulting in 6 total samples.
2014-01-01 | E-GEOD-51409 | biostudies-arrayexpress
Project description: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.
2012-10-01 | GSE40461 | GEO
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
Project description: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. For the series GSE28152, isogenic isolates were sequentially collected from two cystic fibrosis (CF) patients several years apart. The isolates had not been eradicated in the meantime and represent persister strains. One was an Australian Epidemic Strain-1 isolate and the other a non-epidemic strain. Strains were cultured in an artificial sputum medium (ASMDM) closely resembling CF sputum.
2011-07-15 | E-GEOD-28152 | biostudies-arrayexpress
Project description:Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ?anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ?anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ?anr, clinical isolate J215, and J215 ?anr, each in duplicate, by deep sequencing using Illumina HiSeq.
2015-06-29 | E-GEOD-68534 | biostudies-arrayexpress
Project description:Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). The P. aeruginosa CF isolate PASS4 has reduced ability to catabolise various carbon sources however can grow on DNA as a sole carbon source but, with a higher biomass production than P. aeruginosa burns wound, laboratory strain PAO1. Therefore, proteomic profiling of PASS4 and PAO1 was conducted following growth on DNA as a sole carbon source. To compare the protein expression of P. aeruginosa strains PAO1 and PASS4 following growth in DNA, the amino acid, asparagine was used a control condition, as asparagine was one of the amino acids PASS4 could utilise.
2019-06-24 | PXD006742 | Pride
Project description:Although Pseudomonas aeruginosa is an opportunistic pathogen that does not often naturally infect alternate hosts such as plants, the plant-P. aeruginosa model has become a widely recognized system for identifying new virulence determinants and studying pathogenesis of this organism. Here we examine how both host factors and P. aeruginosa PAO1 gene expression are affected in planta after infiltration into incompatible and compatible cultivars of tobacco (Nicotiana tabacum L.) Nicotiana tabacum has a resistance gene (N) against tobacco mosaic virus; and although resistance to PAO1 infection correlated to the presence of a dominant N-gene, our data suggests that it is not a factor in resistance against Pseudomonas. We did observe that the resistant tobacco cultivar had higher basal levels of salicylic acid, and a stronger salicylic acid response upon infiltration of PAO1. Salicylic acid acts as a signal to activate defense responses in plants, limiting the spread of the pathogen and preventng access to nutrients. It has also been shown to have direct virulence modulating effects on P. aeruginosa. We also examined host effects on the pathogen by analyzing global gene expression profiles of bacteria removed from the intracellular fluid of the two plant hosts. We discovered that the availability of micronutrients, particularly sulfate and Pi, are important factors in in planta pathogenesis, and that the amounts of these nutrients made available to the bacteria may in turn have an effect on virulence gene expression. Indeed, there are several reports suggesting that P. aeruginosa virulence is influenced in mammalian hosts by the availability of iron and by levels of O2. Experiment Overall Design: Pseudomonas aeruginosa cells were removed from leaf tissue 24 hours post-infiltration and RNA was directly extracted from these cells. Comparisons are between cells removed from a susceptible cultivar of Nicotiana tabacum (cv. Samsun) and a resistant cultivar (cv. Xanthi). Three biological replicates per cultivar were analyzed.
2008-10-25 | E-GEOD-11544 | biostudies-arrayexpress
Project description:Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome, and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as sulfur source led to a sulfate starvation response, but also to induction of genes involved with type III secretion systems. Experiment Overall Design: Gene expression in exponential-phase cells was analysed using Affymetrix arrays. Sulfur was supplied either as sulfate, or as the non-sulfate S sources cyclamate (sodium cyclohexylsulfamate) and mucin (human colon cell line mucin LS174T). Control experiments were also done with combinations of these sulfur sources. Studies with mucin as sulfur source were carried out with P. aeruginosa E601 (a CF isolate with mucin sulfatase activity) and comparative studies were performed with P. aeruginosa PAO1. Experiments with strain E601 were done in 3-4 fold replication, experiments with strain PAO1 with 2-3 fold replication.
2008-06-16 | E-GEOD-8408 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of farnesol-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: Our RNA-seq results showed that less than 100 genes of P. aeruginosa PAO1 were differentially expressed following farnesol treatment. We found that about 1.7% of all detected genes (96 of 5554 genes) were more than two-fold differentially expressed following farnesol treatment. Conclusions:
2019-10-11 | GSE138731 | GEO
Project description:The purpose of this study was to define the TZD effect in Pseudomonas aeruginosa. Transcriptional profiling of Pseudomonas aeruginosa wild-type strain,reference strain PAO1, as control Vs. PAO1 strain exposed to a final 0.02mM of TZD derivative ((z)-5-octylidenethiazolidine-2,4-dione).
2014-12-03 | E-MTAB-3144 | biostudies-arrayexpress