Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Intestinal 16SrRNA gene sequencing data of GIFT Tilapia

PROVIDER: PRJNA806406 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17999932_1.fastq.gz	Fastqsanger.gz
	SRR17999932_2.fastq.gz	Fastqsanger.gz
	SRR17999933_1.fastq.gz	Fastqsanger.gz
	SRR17999933_2.fastq.gz	Fastqsanger.gz
	SRR17999934_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Project description:GIFT tilapia pooled WGS sequencing

| PRJNA520791 | ENA

Analysis of bacteremia after endoscopic submucosal dissection of the colon using molecular biological technique.

Project description:Interventions: Analysis of bacteremia after ESD of the colon. Primary outcome(s): Identification of bacteremia after ESD testing blood culture and 16SrRNA gene sequencing. Study Design: Single arm Non-randomized

| 2623655 | ecrin-mdr-crc

Nile Tilapia GIFT genome assembly

Project description:Nile Tilapia GIFT genome assembly

| PRJEB48957 | ENA

Identification of potential pathways whereby dietary high fat induced hepatic lipid metabolic disorder of Oreochromis niloticus through long non-coding RNAs

Project description:Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalance and suffer from fatty liver disease during the intensive farming. Long non-coding RNAs (lncRNAs) performed essential roles in varieties of biological processes, including lipid metabolism. However, the lncRNAs regarding hepatic lipid metabolism in tilapia have not been identified. In this study, Illumina sequencing and bioinformatic analysis was performed on the liver of male GIFT juvenile fed with high-fat diet (HFD, 18.5% lipid) or normal-fat diet (NFD, 8% lipid) for 56 days. RNA-seq analyses revealed 299 differentially expressed (DE)-mRNAs and 284 DE-lncRNAs between these two groups. The transcript expression of 16 candidates (eight DE-mRNA and eight DE-lncRNAs) was verified by qRT-PCR, and the results were consistent with those of RNA-seq. Furthermore, 65 cis targets and 3610 trans targets of DE-lncRNAs were predicted. Functional analyses suggested that multiple metabolic pathways was changed in response to high-fat intake, including PPAR signaling pathway, Fatty acid degradation and Fatty acid metabolism, among others. Co-expression networks was constructed and indicated that most lncRNAs interact with numerous mRNAs involved in lipid metabolism, and vice versa. Additionally, expression patterns analysis of three lncRNAs (MSTRG.14598.1, MSTRG.6725.3 and MSTRG.13364.2) and their potential targets (faldh, slc25a48 and fabp7a) associated with PPAR signaling pathway were investigated. Our study provides a basis for further explore the functions of lncRNAs associated with lipid metabolism in tilapia.

2023-09-01 | GSE211712 | GEO

Transcriptome analysis of miRNA–mRNA interactions revealed regulation of multiple signaling pathways in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues under hypoxia stress

Project description:Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. Here, we first examine the hypoxia-induced damage of gill tissue by hematoxylin-eosin staining, and then constructed miRNA and mRNA libraries of GIFT gill tissue at 96h of hypoxia stress by a high-throughput sequencing technology, each library has three biological replicates. Gill lamellae of GIFT showed capillary rupture and red blood cell enlargement and overflow under hypoxia stress. Transcription sequencing results showed that the clean reads of miRNA libraries were 9,627,953-13,544,660; the clean reads of mRNA libraries were 43,817,776-53,130,102. Based on the miRNA-mRNA pairs screening principles and mRNA sequencing results, we selected and verified seven differentially expressed miRNAs and their potential target genes. The sequencing results were consistent with the qRT-PCR validation results. These selected miRNA-mRNA pairs are mainly concentrated in the signaling pathways of immune response and metabolic regulation. This study provides new insights into the mechanisms of fish adaptation under hypoxic stress.

2023-02-22 | GSE145788 | GEO

Growth, blood biochemistry, histology and transcriptomic profile analysis influences liver fat deposition and inflammation process following dietary supplementation of apple peel powder in Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus)

Project description:GIFT is a type of freshwater farmed fish with high economic value and nutritional value. The liver is an important organ of fish metabolism. Once it is damaged or the disease occurs, it will lead to metabolic disorders and decreased disease resistance, and may cause other secondary diseases. In the high-density intensive culture of tilapia, the feed nutrition is not balanced, especially the addition of high-fat feed. High fat content can accelerate the growth of fish, but long-term feeding of high-fat diet can lead to metabolic disorders of fish, accumulation of fat in the body, easy to cause fatty liver, and ultimately death due to liver necrosis or hemorrhage, seriously affecting the breeding benefits. The main purpose of this study was to investigate the effects of apple peel added to feed on liver fat metabolism and fat deposition in tilapia tilapia; use transcriptomics to analyze related signal regulation pathways, focusing on fat metabolism and inflammatory response; and finally screening differentially expressed genes. The development of this study is helpful to understand the molecular mechanism of apple peel extract powder-mediated liver fat metabolism and inflammatory response in GIFT, and relieve liver stress. It also provides theoretical support for the application of apple peel extract powder as a feed additiion in aquatic products.

2019-12-04 | GSE127810 | GEO

Project description:16SrRNA gene sequencing data

| PRJNA821680 | ENA

2023-02-26 | GSE146050 | GEO

fish gut metagenome

Project description:Gastrointestinal microbiome of tilapia (GIFT) in PNG

| PRJNA525298 | ENA

Combined analysis of transcriptome and metabolome in tilapia (GIFT, Oreochromis niloticus) exposed to acute hypoxia stress

Project description:Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. We built control (5mg/l) and hypoxic stress (96h-LH50) groups, and extracted the liver tissues for high-throughput transcriptome and metabolome sequencing. The identification and quantification results of metabolites showed that a total of 19656 metabolites had been obtained, of which 10390 were annotated. There were 3028 differentially expressed (DE) metabolites, of which 1596 metabolites were up-regulated and 1432 metabolites were down-regulated. We obtained 2375 DE genes, of which 1201 genes were up-regulated and 1174 genes were down-regulated. We verified 8 DE genes by quantitative real-time PCR. Our finding reveals the changes in metabolites and genes expression of GIFT and facilitate the understanding of regulatory pathways under hypoxic stress, which will help reduce the damage caused by hypoxic stress during culture.

2021-01-12 | GSE146142 | 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