Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1112337 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Extension of cod-fisheries across northern Europe
| PRJEB52865 | ENA
Project description:Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C. Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry.
2023-08-01 | GSE233737 | GEO
Project description:Population genomics in Atlantic cod, Gadus morhua
| PRJNA78311 | ENA
Project description:Background: In coeliac disease (CoD), the role of B cells has mainly been considered to be production of antibodies. The functional role of B cells has not been analysed extensively in CoD. Methods: We conducted a study to characterize gene expression in B cells from children developing CoD early in life using samples collected before and at the diagnosis of the disease. Blood samples were collected from children at risk at 12, 18, 24 and 36 months of age. RNA from peripheral blood CD19+ cells was sequenced and differential gene expression was analysed using R package Limma. Findings: Overall, we found one gene, HNRNPL, modestly downregulated in all patients (logFC -0·7; q=0·09), and several others downregulated in those diagnosed with CoD already by the age of 2 years. Interpretation: The data highlight the role of B-cells in CoD development. The role of HNRPL in suppressing enteroviral replication suggests that the predisposing factor for both CoD and enteroviral infections is the low level of HNRNPL expression.
2023-02-01 | GSE185503 | GEO
Project description:The aim of the exposure was to study the effects of activation of peroxisome proliferator-activated receptors (PPARs) in Atlantic cod (Gadus morhua), by injecting the fish with the compounds WY-14,643 and GW501516. Using luciferase reporter assay in vitro, we have shown that WY-14,643 activate Atlantic cod Ppara1 and Ppara2, while GW501516 activate Ppara1, Ppara2, and Pparb. The experimental set-up was as follows: Immature cod were injected at day 0 and day 4 with either high dose (40 mg/kg WY-14,643 and 4.0 mg/kg GW501516), low dose (4.0 mg/kg WY-14,643 and 0.4 mg/kg GW501516), or solvent control (10 % DMSO, 90 % teleost saline (2.41 mM KCl, 133.5 mM NaCl, 1.5 mM CaCl2, 0.79 mM MgSO4, 1 mM NaHCO3, 0.5 mM Na2HPO4)). At day 11, liver samples were collected from 9-12 male fish from each group (total of 50 samples). Total RNA was isolated from 50 mg of each sample using TRI reagent (Sigma), and 0.4 μg RNA were sequenced at the Genomics Core Facility at the University of Bergen on Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA, USA).
2022-03-06 | E-MTAB-11490 | biostudies-arrayexpress
Project description:Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if “egg life history traits” can be hidden in egg transcriptomes. To pursue this, salmon and cod eggs were selected due to their largely differencing phenotypes (size, robustness, fresh/marine). An oligo microarray analysis was performed on ovulated eggs from cod (~23 000 genes, n=8) and salmon (~44 000 genes, n=7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated based on official gene symbol to retrieve an orthologous KEGG annotation, in salmon and cod arrays this represented 14009 and 7437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score > 300, resulting in a total of 2354 KEGG annotations (genes) being differently expressed between the species. The most differentially expressed genes in salmon and cod (FD≥2), were used to reveal pathways that were overrepresented in the eggs of each species. This analysis revealed that immune, signal transduction, and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.
2014-08-31 | GSE59877 | GEO
Project description:This study was performed to validate the newly developed CGP Atlantic cod 20K oligonucleotide microarray. Atlantic cod (Gadus morhua) received an intraperitoneal injection of either formalin-killed, atypical Aeromonas salmonicida (Asal) or PBS and transcriptional profiles of spleen tissues from Asal-injected fish were compared to those from pre-injection control fish and PBS-injected control fish. Gene expression profiles resulting from this study were compared to those from suppression subtractive hybridization library studies, that were previously performed on the same samples, and to literature. Gene expression patterns of single genes were confirmed by QPCR analysis. This study has shown that the newly developed CGP Atlantic cod 20K oligo microarray platform is a valuable tool for cod genomic research.
2010-11-05 | GSE22312 | GEO
Project description:Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Four Ppar subtypes from Atlantic cod (Gadus morhua) were recently cloned and characterized. However, the downstream regulatory role of Ppars in cod lipid metabolism is presently not well understood or described. Here we study the involvement of Atlantic cod Ppar subtypes in systemic regulation of lipid metabolism using the model agonists WY14,643, GW501516, and tetradecylthioacetic acid, employing a multiple omics approach after an in vivo exposure situation.
2022-09-20 | PXD031739 | Pride
Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod subpopulation: western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through genome-wide oligonucleotide microarray.
2022-02-02 | GSE195878 | GEO
Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray.
2019-01-21 | GSE122988 | GEO