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Vibrio parahaemolyticus

ABSTRACT: Differential expression analysis of a Vibrio parahaemolyticus ∆rpoN mutant compared to wild-type in minimal media supplemented with glucose or mouse intestinal mucus

PROVIDER: PRJNA377522 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5298500.fastq.gz	Fastqsanger.gz
	SRR5298510.fastq.gz	Fastqsanger.gz
	SRR5298501.fastq.gz	Fastqsanger.gz
	SRR5298511.fastq.gz	Fastqsanger.gz
	SRR5298502.fastq.gz	Fastqsanger.gz

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Differential expression analysis of a Vibrio parahaemolyticus ∆rpoN mutant compared to wild-type in minimal media supplemented with glucose or mouse intestinal mucus

Project description:Vibrio parahaemolyticus is the leading bacterial cause for seafood-related gastroenteritis worldwide. As an intestinal pathogen, V. parahaemolyticus competes with other commensal bacteria for the same pool of nutrients. The major source of nutrition for intestinal bacteria is intestinal mucus. We wanted to determine the expression profile of wild-type V. parahaemolyticus in mouse intestinal mucus and then perform a differential expression analysis in a ∆rpoN deletion mutant.

2020-02-14 | GSE95555 | GEO

Examination of growth mode dependent replication dynamics and expression levels for Vibrio parahaemolyticus RIMD2210633.

Project description:Replication of bacterial chromosomes increases the copy numbers of genes located near the origin of replication relative to genes located near the terminus. Such differential gene dosage is variable and depends on several factors including replication rate, generation time and chromosome size. For vibrios, a diverse family of fast growing marine living gammaproteobacteria, gene dosage effects may be particularly important as they harbour their genome within two differently sized chromosomes. In this series of experiments, gene dosage at the genomic level and its influence on the expression level has been examined in V. parahaemolyticus. For the genomic analyses, gene copy numbers for bacteria in mid-logarithmic phase grown in rich media (Luria-Bertani containing 3% (w/v) NaCl) at two temperatures (37°C or 20°C) or in minimal media (M9 containing 3% (w/v) NaCl and 0.4% (w/v) glucose) were compared against gene copy numbers for non-replicating cells. For expression analyses, cDNA derived from bacteria in mid-logarithmic phase grown in rich broth at two temperatures (37°C or 20°C) or in minimal media were compared against gDNA from non-replicating cells. Also, cDNA derived from early (OD600=0.2) or mid-logarithmic phase bacteria (OD600=0.5) in rich broth at 37°C, were compared against cDNA derived from mid-logarithmic cells in minimal media (OD600=0.5) or cDNA from early stationary phase rich broth cells (OD600=3.0). Keywords: Comparative genomic and/or cDNA hybridization

2008-11-20 | GSE9968 | GEO

Differential expression analysis of a Vibrio parahaemolyticus ∆luxO mutant compared to wild-type in mouse intestinal mucus

2017-01-13 | GSE93547 | GEO

Examination of growth mode dependent replication dynamics and expression levels for Vibrio parahaemolyticus RIMD2210633.

Project description:Replication of bacterial chromosomes increases the copy numbers of genes located near the origin of replication relative to genes located near the terminus. Such differential gene dosage is variable and depends on several factors including replication rate, generation time and chromosome size. For vibrios, a diverse family of fast growing marine living gammaproteobacteria, gene dosage effects may be particularly important as they harbour their genome within two differently sized chromosomes. In this series of experiments, gene dosage at the genomic level and its influence on the expression level has been examined in V. parahaemolyticus. For the genomic analyses, gene copy numbers for bacteria in mid-logarithmic phase grown in rich media (Luria-Bertani containing 3% (w/v) NaCl) at two temperatures (37Â°C or 20Â°C) or in minimal media (M9 containing 3% (w/v) NaCl and 0.4% (w/v) glucose) were compared against gene copy numbers for non-replicating cells. For expression analyses, cDNA derived from bacteria in mid-logarithmic phase grown in rich broth at two temperatures (37Â°C or 20Â°C) or in minimal media were compared against gDNA from non-replicating cells. Also, cDNA derived from early (OD600=0.2) or mid-logarithmic phase bacteria (OD600=0.5) in rich broth at 37Â°C, were compared against cDNA derived from mid-logarithmic cells in minimal media (OD600=0.5) or cDNA from early stationary phase rich broth cells (OD600=3.0). Keywords: Comparative genomic and/or cDNA hybridization Samples of genomic DNA and/or cDNA were labeled with Cy3 and Cy5 and cohybridized on six single arrays.

2010-05-15 | E-GEOD-9968 | biostudies-arrayexpress

Vibrio parahaemolyticus RIMD 2210633 T6SS2 secretome

Project description:Comparative proteomics to identify proteins found in the media of Vibrio parahaemolyticus RIMD 2210633 bacteria with an active T6SS2 compared to bacteria with inactive T6SS2. Bacteria with an active T6SS2 are Vibrio parahaemolyticus RIMD 2210633 inwhich hcp1 was deleted to inactivate T6SS1. T6SS2 inactive bacteria are the former strain with an additional deletion in hcp2. Both strains express TfoX from an arabinose-inducible plasmid to induce T6SS2 activity.

2023-02-05 | PXD037980 | Pride

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [tiling arrays]

Project description:Investigation of whole genome gene expression level in Klebsiella pneumoniae MGH78578 grown up to mid-exponential phase in M9 minimal media supplemented with 0.2% glucose

2012-07-30 | GSE35746 | GEO

Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments

Project description:E. coli K-12 MG1655 was grown on M9 minimal media supplemented with 0.2% w/v glucose, fructose, or acetate. The goal of this study was to determine differentially expressed genes in the different media conditions.

2018-02-02 | GSE108871 | GEO

Vibrio parahaemolyticus RIMD 2210633

Project description:Differential expression analysis of a Vibrio parahaemolyticus ∆luxO mutant compared to wild-type in mouse intestinal mucus

| PRJNA361081 | ENA

Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose

2014-02-05 | GSE46543 | GEO

Transcriptome Analysis of T3SS1 in Vibrio parahaemolyticus

Project description:Comparative transcriptional mRNA profiles were generated of bacterial pathogen Vibrio parahaemolyticus under conditions that induce activity of virulence factor type III secretion system 1 (T3SS1). Induction conditions included growth of the bacteria in Dulbecco's Modified Eagle Medium (DMEM), overexpression of transcriptional activator exsA and contact with HeLa cells in Hank's Balanced Salt Solution (HBSS), while non-inducing conditions included growth in Luria-Bertani medium supplemented with 2.5% (w/v) NaCl (LB-S) and overexpression of transcriptional anti-activator exsD. Transcriptome profiles of induction conditions were cross-compared against background non-inducing conditions and time points during HeLa cell infection (2 hr, 3 hr, 4 hr, 6 hr, 8 hr) were compared against pre-infection (0 hr) to identify genes important in T3SS1 activity and pathogenesis. Duplicate mRNA transcriptome profiles of V. parahaemolyticus grown in T3SS1 inducing (DMEM, exsA expression) and non-inducing (LB-S, exsD expression) conditions as well as during HeLa cell infection (0 hr, 2 hr, 3 hr, 4 hr, 6 hr, 8 hr) were generated by deep sequencing using an Illumina MiSeq

2014-01-21 | E-GEOD-51423 | biostudies-arrayexpress

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