Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Coho salmon low-coverage whole genome re-sequencing

PROVIDER: PRJNA1247473 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33004446_1.fastq.gz	Fastqsanger.gz
	SRR33004446_2.fastq.gz	Fastqsanger.gz
	SRR33004447_1.fastq.gz	Fastqsanger.gz
	SRR33004447_2.fastq.gz	Fastqsanger.gz
	SRR33004448_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Coho Salmon GH Transgenic Study

Project description:Coho Salmon GH Transgenic Study Keywords: other

2005-05-01 | GSE2388 | GEO

Project description:Whole Genome Resequencing in Coho salmon

| PRJNA401427 | ENA

Enhanced transcriptomic responses in the Pacific salmon louse Lepeophtheirus salmonis oncorhynchi to the non-native Atlantic Salmon Salmo salar suggests increased parasite fitness

Project description:This study investigates host-specific gene expression of the Pacific salmon lice, Lepeophtheirus salmonis oncorhynchii, while parasitizing a resistant host (Coho salmon), two susceptible hosts (Atlantic salmon, Sockeye salmon), and a population with-held hosts (starved), over 48 hrs.

2017-01-25 | GSE80220 | GEO

Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

Project description:Background: Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results: We characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions: Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

2024-06-24 | GSE269132 | GEO

Project description:Low-coverage whole-genome re-sequencing of European plaice (Pleuronectes platessa)

| PRJEB36564 | ENA

Chromosomal microarray analysis for validation of the WGS-based CNV detection results in recurrent miscarriage couples

Project description:In order to validate of CNV detection from low-coverage whole-genome sequencing in the blood samples from recurrent miscarriage couples, we employed a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach as chromosomal microarray analysis (CMA) in present study for a cohort of 78 DNA samples from blood. CMA results were compared with low-coverage whole-genome sequencing detection results. 100% consistency was obtained in pathogenic or likely pathogenic CNVs detection.

2017-11-01 | GSE83941 | GEO

Profiling of Salmo salar in two Atlantic salmon types, a wild type versus transgenic.

Project description:The influence of GH transgenesis on liver gene expression in coho salmon was examined. Gene expression in livers of transgenic salmon on a restricted ration (R) was compared to that in livers of nontransgenic control salmon (C). Keywords: Transcript profile

2005-12-30 | GSE3475 | GEO

Identification of driver genes in uterine leiomyosarcoma: low-coverage WGS

Project description:Low coverage whole-genome sequencing have been performed on uterine leiomyosarcoma to uncovered novel potential driver genes and recurrently affected pathways.

2018-07-02 | E-MTAB-5763 | biostudies-arrayexpress

Project description:low-coverage re-sequencing of Carassius auratus

| PRJNA596626 | ENA

Mapping meiotic crossovers in Arabidopsis using low-coverage whole-genome sequencing

Project description:Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.

2015-10-15 | E-MTAB-3926 | biostudies-arrayexpress

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