Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-tissue transcriptome profiling of North American derived Atlantic salmon

ABSTRACT: Multi-tissue transcriptome profiling of North American derived Atlantic salmon

PROVIDER: PRJNA470665 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7139950_1.fastq.gz	Fastqsanger.gz
	SRR7139950_2.fastq.gz	Fastqsanger.gz
	SRR7139960_1.fastq.gz	Fastqsanger.gz
	SRR7139960_2.fastq.gz	Fastqsanger.gz
	SRR7139970_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

Multi-tissue transcriptome profiling of North American derived Atlantic salmon

Project description:The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.

2018-08-22 | GSE114247 | GEO

Distinct early-life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations

Project description:Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disrupts local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic risks posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of late sac fry of a European (EO) farmed (“StofnFiskur”, Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected fewer differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the fitness of wild populations.

2022-03-11 | GSE184425 | GEO

Whole Genome Resequencing in North American Atlantic salmon

Project description:We performed high coverage whole genome re-sequencing of 80 North American Atlantic salmon individuals from three aquaculture stocks that are propagated in the USDA-ARS National Cold Water Marine Aquaculture Center (NCWMAC). The sequence data was used for SNP discovery and the resulting SNP database provides an important resource for a new high density SNP array design and other SNP genotyping platforms used in various genetic and genomics studies of North American Atlantic salmon.

2019-09-03 | PRJEB34225 | EVA

Salmo salar strain:St. John River | breed:North American Atlantic salmon

Project description:Salmo salar strain:St. John River | breed:North American Atlantic salmon Genome sequencing and assembly

| PRJNA759632 | ENA

Atlantic salmon

Project description:Atlantic salmon Metagenome

| PRJNA656628 | ENA

Atlantic salmon gastric mucosa LC-MSMS

Project description:The Atlantic salmon (Salmo salar) genome contains 10 chitinase encoding genes, but little is known about the function of these chitinases. Three of the chitinase genes have previously been shown to be expressed in the stomach tissue of Atlantic salmon. In the current study we show that the protein products of these genes, the family 18 glycoside hydrolase (GH18) chitinases, Chia.3, Chia.4 and Chia.7 are secreted into the stomach mucosa and are amongst the most abundant proteins in this matrix.

2022-05-08 | PXD030291 | Pride

Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in Atlantic salmon

Project description:This SuperSeries is composed of the following subset Series: GSE26981: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in skin of Atlantic salmon GSE26984: Responses to ectoparasite salmon louse (Lepeophtheirus salmonis) in spleen of Atlantic salmon Refer to individual Series

2011-02-03 | E-GEOD-27013 | biostudies-arrayexpress

Conservation genomics of Atlantic salmon

Project description:This SuperSeries is composed of the following subset Series: GSE19111: Conservation genomics of Atlantic salmon (Year One) GSE19119: Conservation genomics of Atlantic salmon (Year Two) Refer to individual Series

2010-05-19 | E-GEOD-19170 | biostudies-arrayexpress

Responses of Atlantic salmon to vaccination and challenge with salmon alphavirus (SAV) and Moritella viscosa

Project description:Salmon alphavirus (SAV) and Moritella viscosa causing respectively pancreatic disease and winter ulcer are among the most important pathogens threatening Atlantic salmon aquaculture. Fish is protected by vaccination with different rate of success. Here, responses to vaccination were assessed followed with pathogen challenges of vaccinated salmon and saline injected control.

2021-04-23 | GSE173130 | GEO

single nuclei RNAseq data from Atlantic salmon (Salmo salar) gill

Project description:An snRNAseq analysis of the Atlantic salmon gill to characterise its cellular complexity and development.

2021-02-22 | GSE166686 | GEO