Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Vibrio parahaemolyticus O- and K-antigen serotyping

ABSTRACT: Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen serotyping

PROVIDER: PRJEB39490 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR5319150.fastq.gz	Fastqsanger.gz
	ERR5319160.fastq.gz	Fastqsanger.gz
	ERR5319180_1.fastq.gz	Fastqsanger.gz
	ERR5319180_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 70

Similar Datasets

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

Vibrio parahaemolyticus BB22OP T6SS2 secretome

Project description:Compare the secreted proteins of a wild-type Vibrio parahaemolyticus strain with those of a mutant in hcp2, rendering the T6SS2 inactive

2023-02-05 | PXD037864 | Pride

Transcriptome analysis of pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Vibrio parahaemolyticus inoculation

Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a transcriptome analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.

2020-06-18 | GSE107697 | GEO

OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22

Project description:Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed. Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes. In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads. A comparison with the previous microarray data showed good correlation between the shared genes. The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed. Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR. The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics. One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs. The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus. The wild type Vibrio parahaemolyticus BB22 strain LM5312 and an opaR deletion strain LM5674 were analyzed for mRNA expression using RNA-Seq.

2013-12-31 | E-GEOD-53639 | biostudies-arrayexpress

Vibrio parahaemolyticus gene expression affected by 0.04% bile

Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. Strain RIMD 2210633, the wild type strain of the organism, causes acute gastroenteritis in humans. Human intestinal factor bile often affects the global gene regulation in some species of enteropathogenic bacteria. To determine the genes in V. parahaemolyticus that respond to bile, we investigated the differences in the transcriptomes of the wild type strain and the vtrA-null strain grown in Luria-Bertani medium cultivated with or without 0.04% crude bile. The vtrA gene encodes the previously identified T3SS2 regulator. Our goal is to demonstrate bile regulon controlled by VtrA in V. parahaemolyticus.

2010-10-10 | GSE21666 | GEO

OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22

2013-12-31 | GSE53639 | GEO

Transcriptomic analysis of response of Vibrio parahaemolyticus to excess copper.

Project description:We studied the transcriptome changes of Vibrio parahaemolyticus under normal culture condition and copper stress by RNA sequencing. The data showed that genes in copA and cusFABC operon were significantly upregulated by copper.

2024-08-01 | GSE268489 | GEO

Identification of differentially expressed host microRNAs that respond to Vibrio parahaemolyticus infection in the pacific white shrimp Litopenaeus vannamei.

Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a miRNA-seq analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.

2020-06-18 | GSE107696 | GEO

RNA sequencing analysis of the genes regulated by ZntR in Vibrio parahaemolyticus.

Project description:The transcriptome of the wild type strain and ΔzntR of Vibrio parahaemolyticus was compared by RNA sequencing analysis. The data revealed that some genes, such as zntA, were significantly differentially expressed in the mutant.

2024-05-31 | GSE268232 | GEO

ChIP-seq identified the regulation of genes by the quorum-sensing regulator OpaR in Vibrio parahaemolyticus

Project description:We report that ChIP-seq analyses of the quorum-sensing regulator OpaR at late-log and stationary phase in Vibrio parahaemolyticus

2020-10-27 | GSE122479 | GEO

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