Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional response of Pseudomonas aeruginosa to treatment with the antibacterial compound SPI031

ABSTRACT: A transcriptome analysis was performed using RNA sequencing to uncover the cellular responses of Pseudomonas aeruginosa PA14 to SPI031. To assess the direct effects of the compound on cellular processes, the transcription profile was determined from cells treated for 5 min with a sub-inhibitory concentration of SPI031 (0.2x MIC).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Pseudomonas aeruginosa UCBPP-PA14

SUBMITTER: Bram Weytjens

PROVIDER: E-MTAB-4691 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

small RNA-Seq showing transfer of bacterial outer membrane vesicle (OMV) sRNA to host airway epithelial cells

Project description:This study is the first to show transfer of regulatory bacterial sRNAs from bacterial OMVs to host cells. Demonstration of transfer of bacterial sRNA from Pseudomonas aeruginosa OMVs to host cells in two cell types. RNA isolated from PA14 OMV exposed primary human bronchial epithelial cells or CFBE41o- bronchial epithelial cells as well as unexposed control cells was analyzed by small RNA-Seq. Primary cell exposures were performed on two donors and exposures of CFBE41o- cells were done in triplicate.

2016-05-13 | E-GEOD-80421 | biostudies-arrayexpress

Comparative Profiling of Pseudomonas aeruginosa Strains Reveals Differential Expression of Novel Unique and Conserved Small RNAs

Project description:Pseudomonas aeruginosa is a highly adaptable bacterium which thrives in a broad range of ecological niches and can infect multiple hosts as diverse as plants, nematodes and mammals. In humans, it is an important opportunistic pathogen. This wide adaptability correlates with its broad genetic diversity. In this study, we used a deep-sequencing approach to explore the complement of small RNAs (sRNAs) in P. aeruginosa as the number of such regulatory molecules previously identified in this organism is relatively low, considering its genome size, phenotypic diversity and adaptability. We have performed a comparative analysis of PAO1 and PA14 strains which share the same host range but differ in pathogenicity, PA14 being considerably more virulent in several model organisms. Altogether, we have identified more than 150 novel candidate sRNAs and validated a third of them by Northern blotting. Interestingly, a number of these novel sRNAs are strain-specific or showed strain-specific expression, strongly suggesting that they could be involved in determining specific phenotypic traits. 2 cDNA samples (enriched for different size ranges ) from each of two strains of Pseudomonas aeruginoasa (PAO1 and PA14) were sequenced with the Roche 454 technology

2012-06-04 | E-GEOD-36340 | biostudies-arrayexpress

Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa

Project description:LFQ proteome datasets of Pseudomonas aeruginosa type strain PA14 cultured at different enviromental conditions: Exponential-, transition- and stationary(12 h and 24 h)growth phases. Biofilm (24 h and 48 h), low osmolarity conditions (control = exponential phase), iron starvation and respective control, Sub-MIC ciproflox treatment and respective control.

2018-11-20 | PXD010200 | Pride

The P. aeruginosa PA14 transcriptome recorded under 14 different experimental conditions

Project description:We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). Most of the genes were also differentially regulated upon sigma factor hyper expression and/or inactivation (GEO accession number GSE54999) and many of those belonged to primary alternative sigma factor regulons. The samples of P. aeruginosa PA14 wild type strain were cultivated under 14 different experimental conditions and were analyzed by RNA-seq. For each condition, at least two biological replicates were generated Please note that PA14 is our standard lab strain used for all generated data in this records. There is no mutation introduced for any of those experiments, and thus, the descriptions only highlight the growth conditions.

2015-06-16 | E-GEOD-55197 | biostudies-arrayexpress

RNA-seq study of major P.aeruginosa PA14 transcription factors

Project description:Gene regulation via transcription factors influences the metabolic, adaptive and pathogenic capabilities of the organism. We report the transcriptomes of the mutants of six major P. aeruginosa PA14 trancription factors - RhlR, LasR, Anr, GacA, FleQ and CbrB. The P. aeruginosa PA14 transposon mutants were analyzed by RNA-seq. All samples were cultivated in LB medium until reaching an OD600 of 2.0. For each biological replicate, three cultures were pooled for RNA extraction, library preparation and sequencing.

2016-03-01 | E-GEOD-55328 | biostudies-arrayexpress

P. aeruginosa PA14 WT in LB medium vs in LB with 10 mM adenosine medium

Project description:To investigate the impact of adenosine on gene expression of wild-type PA14. To investigate the impact of adenosine on gene expression of wild-type PA14, cells were harvested after incubating for 7 h in LB medium and LB with 10 mM adenosine medium, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA.

2012-05-22 | E-GEOD-29665 | biostudies-arrayexpress

Proteomics of Pseudomonas aeruginosa PAO1 and PA14

Project description:Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms, and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we find that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains, to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that post-transcriptional regulation is important for understanding the discordance between mRNA and protein abundance.

2014-05-08 | PXD000684 | Pride

Genotyping of twenty Pseudomonas aeruginosa strains

Project description:20 P. aeruginosa strains were genotyped using a custom spotted oligo array (Ausubel P. aruginosa genotyping 4.8K v1), which included primarily oligos for genes present in strain PA14 but absent in PAO1, and oligos for genes present in PAO1 but absent in PA14 (as well as controls).

2006-10-06 | E-MEXP-824 | biostudies-arrayexpress

Cross-regulation between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa

Project description:Two-component systems (TCS) serve as basic stimulus-response coupling mechanisms to allow organisms to sense and respond to a large variety of environmental conditions. In the opportunistic pathogen Pseudomonas aeruginosa, more than 100 genes encode TCS components. To avoid unwanted cross-talk between TCSs, the signaling cascades are usually very specific, with one sensor talking to its cognate response regulator. However, cross-regulation may provide effective means to integrate different environmental stimuli into a harmonized output response and thus to coordinate gene expression in response to complex and challenging habitats. Here, we applied a protein-fragment complementation assay (PCA) and identified a direct interaction of two response regulators of the OmpR/PhoB subfamily, namely PhoB and TctD in P. aeruginosa in vivo. Transcriptional profiling and ChIP-seq analysis uncovered adjacent bipartite binding motifs of the two response regulators in 8 promoter regions, of which 6 showed a common PhoB-TctD binding motif with a fixed spacing between the two motifs. We further demonstrate that phosphate limitation exhibits a PhoB-dependent activating activity on the expression of those genes, whereas the presence of a preferred carbon source inhibits gene expression in a TctD-dependent manner. Thus, the perception and the integration of two important environmental signals are achieved by a titration of the relative amounts of two phosphorylated response regulators that inversely regulate a common subset of genes. In conclusion, our results shed light on the general principles underlying two-component signal transduction pathways and the exploitation of cross-regulation to adapt bacterial behavior to complex environments. Transcriptome profiling of the UCBP-PA14 phoB and tctD mutants complemented by phoB ChIP-seq experiments.

2015-06-08 | E-GEOD-64056 | biostudies-arrayexpress

Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant

Project description:Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C.

2009-05-23 | E-GEOD-13871 | 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