Generation and characterization of the Arctic charr multi-organ transcriptome
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REPOSITORIES: ENA
Dataset's files
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| ERR868014.fastq.gz | Fastqsanger.gz |
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Project description:We report here the release of a multi organ transcriptome developped for the Arctic char Salvelinus alpinus. This reference set was obtained using the 454 GS FLX+ technology. A pool of one-year-old, immature offspring of wild, anadromous Arctic charr originating from Lake Varflusjoen, Svalbard (79oN), including both lean and fat individuals, and three-years-old mature offspring of charr originating from Lake Vårflusjøen, North-Norway (70oN) was sampled. In order to maximize the diversity of expressed transcripts, we sampled a variety of organs and tissues; the whole brain, gill and head kidney and pieces of the liver, gonad, abdominal fat and muscle.
2016-08-18 | E-MTAB-3522 | biostudies-arrayexpress
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general.
2011-06-01 | GSE26306 | GEO
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general. 18 microarray slides representing 6 individuals from 3 treatment groups (Intolerant, Tolerant and Control). One test cDNA labeled with cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide Reference design: 18 slides (6 x Tolerant fish, 6x Intolerant fish, 6x Control fish) were used.
2011-06-01 | E-GEOD-26306 | biostudies-arrayexpress
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.
2011-07-05 | GSE29610 | GEO
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions. 24 microarray slides representing 6 individuals from 4 treatment groups (Control, During, After and Recovery). One test cDNA labeled with Cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide. Reference design: 6x control fish, 6x group D fish, 6x group A fish, 6x group R fish.
2011-07-05 | E-GEOD-29610 | biostudies-arrayexpress
Project description:Arctic charr exposed to acute thermal stress
| PRJNA136745 | ENA
Project description:The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.
2020-04-30 | E-MTAB-8962 | biostudies-arrayexpress
Project description:Conservation genomics of Arctic charr
| PRJEB62707 | ENA
Project description:Estrogen-triggered Monkey Multi-Organ Cell Atlas
| PRJNA1019778 | ENA
Project description:Cellular senescence is associated with aging but also impacts various physiological and pathological processes such as embryonic development and wound healing. Factors secreted by senescent cells can affect their microenvironment, including local spreading of senescence. Acute severe liver disease is associated with hepatocyte senescence and frequently progresses to multi-organ failure. Why the latter occurs is poorly understood however, the presence of hepatic senescence is associated with poor prognosis and extrahepatic organ failure in acute liver disease. Here, using genetic mouse models of hepatocyte-specific senescence, we demonstrate senescence development in extrahepatic organs and associated organ dysfunction in response to liver senescence. In patients with acute indeterminate hepatitis, the extent of hepatocellular senescence predicts the occurrence of extrahepatic dysfunction, need for liver transplantation and mortality. We identify the Transforming Growth Factor Beta (TGFbeta) pathway as a critical mediator of systemic spread of senescence and TGFbeta inhibition blocks senescence transmission to other organs preventing renal dysfunction. Our results highlight the systemic consequences of organ-specific senescence which, independent of aging, contributes to multi-organ dysfunction.
2024-08-23 | GSE267196 | GEO