Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Bacterial Community Composition in Shrimp Litopenaeus Vannamei during White Faeces Disease Events

PROVIDER: PRJEB37200 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3986940_1.fastq.gz	Fastqsanger.gz
	ERR3986940_2.fastq.gz	Fastqsanger.gz
	ERR3986950_1.fastq.gz	Fastqsanger.gz
	ERR3986950_2.fastq.gz	Fastqsanger.gz
	ERR3986960_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 160

Similar Datasets

Shrimp transcriptome analysis after exposure to recombinant Vibrio parahaemolyticus PirA and PirB toxins

Project description:Vibrio parahaemolyticus is a Gram-negative bacterium commonly found in marine and estuarine environments. Acute hepatopancreatic necrosis disease (AHPND) caused by this bacterium is an ongoing problem among shrimp farming industries. V. parahaemolyticus proteins PirA and PirB have been determined to be major virulence factors that induce AHPND. In this study, Pacific white shrimp (Litopenaeus vannamei) were challenged with recombinant PirA and PirB by a reverse gavage method and then at 30 m, 1, 2, 4, and 6 h time points, the hepatopancreas of five individual shrimp were removed and placed into RNA later. We conducted RNA sequencing of the hepatopancreas samples from a no PirA/B control (n = 5) and PirA/B-treated shrimp at the different time intervals (n=5). We evaluated the different gene expression patterns between the time groups to the control with a focus on identifying differences in innate immune function.

2023-05-05 | GSE200137 | GEO

Identification of genes associated with resistance to acute hepatopancreatic necrosis disease (AHPND) in Litopenaeus vannamei

Project description:Acute hepatopancreatic necrosis disease (AHPND) is a shrimp farming disease, caused by a pathogenic Vibrio parahaemolyticus carrying a plasmid encoding Vp_PirAB-like toxin (VpAHPND). Whiteleg shrimp, Litopenaeus vannamei were fed food pellets containing formalin-killed VpAHPND (FKC-VpAHPND) to select for toxin resistance. To identify genes associated with Vp_PirAB-like toxin resistance, total RNA was sequenced to identify differentially expressed genes (DEGs) in the stomach and hepatopancreas among surviving shrimp (sur-FKC), AHPND-infected shrimp (Vp-inf) and normal shrimp (control). From a total of 79,591 genes, 194 and 224 DEGs were identified in the stomach and hepatopancreas transcriptomes, respectfully. The expressions of DEGs were validated by qPCR of ten genes. Only one gene, a gene homologous to L vannamei anti-lipopolysaccharide factor AV-R isoform (LvALF AV-R), was expressed significantly more strongly in sur-FKC than in the other groups. The association of LvALF AV-R expression and toxin resistance was affirmed from the surviving shrimp in a second-trial of FKC-VpAHPND feeding. These results suggest that LvALF AV-R may be involved in shrimp defense mechanisms against Vp_PirAB-like toxin virulence.

2019-01-01 | GSE104715 | GEO

Effect of diurnal oxygen variation on gene expression in Pacific white shrimp reared in green water system tanks

Project description:World aquaculture production of the Pacific white shrimp (Litopenaeus vannamei) is estimated to account for 80% of the total shrimp produce worldwide. The global demand for shrimp has driven the industry to utilize and rely on semi-intensive and intensive shrimp systems. In the United States, Pacific white shrimp production can take place in semi-intensive earthen ponds, recirculating aquaculture systems (RAS), biofloc technology and green water. In this study, the effects of lowering dissolved oxygen conditions in outdoor green water tanks on global gene expression is examined. Tissue samples from the gill and intestine were collected for gene expression analysis via RNA sequencing. Among all comparisons, RNA sequencing revealed the up-regulation of a single gene: hydroxyacid oxidase 1 gene. The HOA1 gene was found to be 7-fold higher in the intestine sample at the medium aeration level compare to that of the high (control) level. The HAO1 gene, also known as glycolate oxidase 1 (GOX1) is a gene related to the 2-hydroxyacid oxidase enzyme that is part of the oxidoreductase family and plays a role in glyoxylate and dicarboxylate metabolism. The identification of a single differentially expressed gene across all analyzed samples suggests that Pacific white shrimp exposed to lowering dissolved oxygen set points does not induce global changes in gene expression at these levels.

2025-07-17 | GSE281217 | GEO

Project description:White leg shrimp (Litopenaeus vannamei) larviculture

| PRJNA637486 | ENA

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

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

Project description:Bacterial population on Pacific white shrimp Litopenaeus vannamei culture systems

| PRJNA949781 | ENA

Project description:Pacific white shrimp (Litopenaeus vannamei) gut microbiota

| PRJNA839154 | ENA

Taura Syndrome Virus or Yellow Head Virus infection in two strains of L. vannamei different in their resistance to TSV

Project description:The transcriptomic response of two strains of the Pacific whiteleg shrimp, different in their resistance to Taura Syndrome Virus (TSV), in response to infection with TSV and Yellow Head Virus (YHV). Changes in gene expression in the shrimp’s hepatopancreas were assessed using a cDNA microarray containing 2,469 putative unigenes. The patterns of gene expression between the shrimp strains were considerably similar, except for the more advanced stages of Taura Syndrome. Between the different treatments approximately 250 genes were differently expressed. The most advanced stages of YHV infection showed the highest number of differently expressed genes. During infection there were profound changes in the expression of genes related to lipid and protein metabolism, cellular trafficking, immune defense and stress response. Keywords: Disease state analysis, disease resistance There were 5 biological replicates for each of the groups in this experiment. Also, two strains of Litopenaeus vannamei were used: a strain resistant to TSV and a strain susceptible to TSV (Kona line). The treatments consisted of injecting both strains with 60mL of a shrimp extract made from shrimp previously injected with either a SPF shrimp extract (1x10-4), Taura Syndrome Virus (1x10-5) or Yellow Head Virus (1x10-4). The 2 initial control groups were composed of hepatopancreas samples from both strains prior the injections. Samples were also collected from at days 1 and 2 from both strains from the 3 different treatments (control, TSV and YHV).

2009-10-23 | E-GEOD-13354 | biostudies-arrayexpress

Global Proteome in Litopenaeus vannamei

Project description:The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, usually suffered from chilling stress in China. In order to reveal inner proteomics mechanism of chilling tolerance, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, chilling-tolerant GH2 and chilling-sensitive GH1 under normal temperature 28°C, chilling stress 16°C, and 16°C recovered to 28°C, respectively.

2018-05-25 | PXD009889 |

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