Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Pseudomonas aeruginosa to investigate the toxicogenomic Effects of Chlorhexidine diacetate

ABSTRACT: In the present study, we employed Affymetrix Pseudomonas aeruginosa GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Pseudomonas aeruginosa to Chlorhexidine diacetate, which involved initial growth inhibition and metabolism. Experiment Overall Design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Chlorhexidine diacetate. We calculated fold change as the ratio between the signal averages of three untreated (control) and three chlorhexidine diacetate-treated (experimental) cultures for 0, 10 and 60 min exposures.

ORGANISM(S): Pseudomonas aeruginosa

SUBMITTER: Chantal Wheko Nde

PROVIDER: E-GEOD-14253 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Pseudomonas aeruginosa treated with hydrogen peroxide

Project description:Background: Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. Results: Herein, we performed a genome-wide transcriptome analysis of the cellular responses to hydrogen peroxide in order to determine a more complete picture of how oxidative stress-induced genes are related and regulated. Our data reinforce the previous conclusion that DNA repair proteins and catalases may be among the most vital antioxidant defense systems of P. aeruginosa. Our results also suggest that sublethal oxidative damage reduces active and/or facilitated transport and that intracellular iron might be a key factor for a relationship between oxidative stress and iron regulation. Perhaps most intriguingly, we revealed that the transcription of all F-, R-, and S-type pyocins was upregulated by oxidative stress and at the same time, a cell immunity protein (pyocin S2 immunity protein) was downregulated, possibly leading to self-killing activity. Conclusions: This finding proposes that pyocin production might be another novel defensive scheme against oxidative attack by host cells. Experiment Overall Design: We conducted four and five independent microarray experiments with biological replicates in the absence (control) and the presence (experimental) of hydrogen peroxide, respectively.

2007-07-19 | E-GEOD-3090 | biostudies-arrayexpress

Transcription profiling of Pseudomonas aeruginosa response to odium hypochlorite antimicrobial mechanisms

Project description:In the present study, we employed Affymetrix Pseudomonas aeruginosa GeneChip arrays to investigate global gene expression profiles during the cellular response of Pseudomonas aeruginosa to sodium hypochlorite Experiment Overall Design: We calculated fold change as the ratio between the signal averages of four untreated (control) and five sodium hypochlorite-treated (experimental) cultures for 20 min exposure.

2008-06-15 | E-GEOD-7402 | biostudies-arrayexpress

Microarray Analysis of Toxicogenomic Effects of Ortho-Phenylphenol on Staphylococcus aureus

Project description:In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to Ortho-Phenylphenol, which involved initial growth inhibition and metabolism. Keywords: Time course We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Ortho-Phenylphenol. We calculated fold change as the ratio between the signal averages of five untreated (control) and five ortho-phenylphenol-treated (experimental) cultures for 0, 20 and 60 min exposures.

2008-04-01 | E-GEOD-10605 | biostudies-arrayexpress

Transcription profiling of Pseudomonas aeruginosa exposed to toxicogenomic effects of ortho-phenylphenol

Project description:In the present study, we employed Affymetrix Pseudomonas aeruginosa GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Pseudomonas aeruginosa to ortho-phenylphenol, which involved initial growth inhibition and metabolism. Experiment Overall Design: We conducted four independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of ortho-phenylphenol. We calculated fold change as the ratio between the signal averages of four untreated (control) and four ortho-phenylphenol-treated (experimental) cultures for 0, 20 and 60 min exposures.

2008-06-11 | E-GEOD-10604 | biostudies-arrayexpress

Transcriptomics analysis of E. faecalis V583 exposed to subinhibitory concentration of chlorhexidine

Project description:The vancomycin resistant strain V583 was exposed to subinhibitory concentration of chlorhexidine. E. faecalis V583 cells were collected at 15 minutes after chlorhexidine addition and without chlorhexidine, for RNA extraction and hybridization on Affymetrix microarrays.

2017-01-11 | E-MTAB-5181 | biostudies-arrayexpress

Microarray Analysis of Toxicogenomic Effects of Chlorhexidine diacetate on Pseudomonas aeruginosa

2009-01-10 | GSE14253 | GEO

Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant

Project description:Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (M-bM-^IM-%2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7. The total mRNA extracted from Escherichia coli O157:H7 Xuzhou21 and its plasmid cured strain Xuzhou21m were sequenced using Illumina.

2013-03-05 | E-GEOD-44846 | biostudies-arrayexpress

Response of Burkholderia cenocepacia J2315 to subinhibitory concentration of chlorhexidine

Project description:Burkholderia cenocepacia J2315 was grown in LB broth with and without the presence of the desinfectant chlorhexidine in the subinhibitory concentration of 5mg/L. Four biological replicates for each control and test conditions were performed. The experiment was designed as a direct comparison with dye swap of two replicates.

2012-05-10 | E-MEXP-3207 | biostudies-arrayexpress

Escherichia coli K-12: 0%, 10% and 30% hydrogen peroxide (H2O2) treatments, in wild type and luxS mutants

Project description:Transcripitonal profiling of Escherichia coli K-12 W3110 comparing wild type and luxS mutants without or with 10%, 30% H2O2 treatments, two biological replicates for each condition two-variables experiments: samples without or with treatment of 10% or 30% H2O2 for 30min; wild type and luxS mutants

2015-05-19 | E-GEOD-38186 | biostudies-arrayexpress

Transcriptomic analysis of chlorhexidine shock in Acinetobacter baumannii

Project description:In this study the transcriptomic changes occurring in A. baumannii ATCC 17978 in response to shock treament using the biocide chlorhexdine were determined. A. baumannii ATCC 17978 cells were grown at 37Â°C with shaking (200rpm) in 35mL cultures in MH broth to OD600=0.75, at which time they were split into 15mL cultures. One 15mL sample was treated with 4Âµg/mL chlorhexidine (0.5x MIC), whereas the other was not treated and used as a reference. Cultures were allowed to grow for a further 30 mins (to an average final OD600= ~1.35 for untreated cells and 1.25 for chlorhexidine treated samples), when cells were harvested by centrifugation and immediately suspended in Trizol reagent (Invitrogen). Total RNA was extracted using the PureLinkTM Micro-to-Midi Total RNA Purification kit (Invitrogen), incorporating an on-column DNAseI (Invitrogen) digestion. The experiment included using four grids of a custom Agilent 8 x 15000 spot microarray. Three biological replicates and one flip dye experiment.

2013-12-03 | E-GEOD-51525 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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