Ontology highlight
ABSTRACT:
PROVIDER: PRJNA892473 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21981300_1.fastq.gz | Fastqsanger.gz | |||
| SRR21981300_2.fastq.gz | Fastqsanger.gz | |||
| SRR21981301_1.fastq.gz | Fastqsanger.gz | |||
| SRR21981301_2.fastq.gz | Fastqsanger.gz | |||
| SRR21981302_1.fastq.gz | Fastqsanger.gz |
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Project description:We investigated whether exposure to a captive environment during maturation influenced gamete DNA methylation for wild Atlantic Salmon individuals. We then investigated whether these parental effects were detectable in an F1 generation reared in a common environment. We associated DNA methylation with growth and fitness-related phenotypes and demonstrated that intergenerational effects of hatchery exposure during maturation of the parental generation influence fitness-related methylation patterns in the F1 generation.
2020-11-26 | GSE162129 | GEO
Project description:Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs: in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing at the level of the transcriptome in Atlantic salmon (Salmo salar). Full siblings were reared in either a M-bM-^@M-^\simpleM-bM-^@M-^] environment devoid of structure or a M-bM-^@M-^\complexM-bM-^@M-^] environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcription in head tissues using the cGRASP-designed Agilent 4M-CM-^W44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented, several of which are associated with mitosis/cell cycle and muscle and heart development. However, there were also pronounced differences among families in gene transcriptional response to rearing environment, with the number of genes significantly differentially transcribed by juveniles in our independent analyses of each family ranging from zero to 3445 (FDR of 5%). Overall, our results suggest that rearing environment enrichment can profoundly change patterns of gene transcription during salmon development, but that the degree of response depends on genetic background. This was a two-condition experiment in which a total of 30 RNA samples isolated from the heads of developing salmon were analysed: 15 juveniles reared in a traditional hatchery environment and 15 reared in a hatchery environment enriched with gravel substrate.
2014-12-10 | E-GEOD-63982 | biostudies-arrayexpress
Project description:Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs: in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing at the level of the transcriptome in Atlantic salmon (Salmo salar). Full siblings were reared in either a “simple” environment devoid of structure or a “complex” environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcription in head tissues using the cGRASP-designed Agilent 4×44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented, several of which are associated with mitosis/cell cycle and muscle and heart development. However, there were also pronounced differences among families in gene transcriptional response to rearing environment, with the number of genes significantly differentially transcribed by juveniles in our independent analyses of each family ranging from zero to 3445 (FDR of 5%). Overall, our results suggest that rearing environment enrichment can profoundly change patterns of gene transcription during salmon development, but that the degree of response depends on genetic background.
2014-12-10 | GSE63982 | GEO
Project description:This study investigates the baseline or inducible differences in between populations of Atlantic salmon lice Lepeophtheirus salmonis with differing levels of resistance to the parasiticidal drug emamectin benzoate (EMB), as well as the induced effects of EMB exposure to Pacific salmon lice. F1 generation lice were exposed in bioassays to a dilution series of emamectin benzoate.
2014-11-17 | GSE56024 | GEO
Project description:We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings. We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration. Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill Na+/K+-ATPase activity development, which then declined into autumn. In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr. Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts. Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status. By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics. We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways. Non-migrating and migrating natural subyearling fall Chinook salmon were collected from the Snake River. Non-migrating natural subyearling fall Chinook salmon were collected from the Clearwater River. Twelve fish were collected at each of four different time points for a total of 48 fish. Total RNA was extracted from the liver of each fish. Equal amounts of RNA from three fish were pooled to create four pools of RNA per time point. Each RNA pool was hybridized to an array for a total of 16 arrays with four arrays per time point.
2014-06-20 | E-GEOD-58670 | biostudies-arrayexpress
Project description:We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings. We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration. Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill Na+/K+-ATPase activity development, which then declined into autumn. In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr. Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts. Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status. By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics. We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways.
2014-06-20 | GSE58670 | GEO
Project description:A total of 55 individuals were analysed: 15 migratory brown trout (Salmo trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Chevenne river, and 10 Atlantic salmon (S. salar) individuals of a hatchery strain. For each individual, RNA was isolated twice from different parts of the same tissue, independently reverse transcribed into Cy3-labeled cDNA and then probed on two different slides, which leads to total of 110 single slide experiments.
2006-03-27 | E-MEXP-123 | biostudies-arrayexpress
Project description:Transcripts of the gill epithelium from three different stocks of Atlantic salmon (Salmo salar) migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt) using the 16K GRASP cDNA microarray platform.
2010-06-01 | E-MEXP-2210 | biostudies-arrayexpress
Project description:This study investigates the baseline or inducible differences in between populations of Atlantic salmon lice Lepeophtheirus salmonis with differing levels of resistance to the parasiticidal drug emamectin benzoate (EMB), as well as the induced effects of EMB exposure to Pacific salmon lice. F1 generation lice were exposed in bioassays to a dilution series of emamectin benzoate. Two separate experiments were conducted, one for Atlantic and one for Pacific salmon lice (to be analyzed separately). Atlantic pre-adult salmon lice, separated into male and female, and sensitive or resistant to EMB populations, and exposed to a dilution series: 0 (control), 0.1, 25, 300, and 1000 parts per billion EMB. For each combination four biological replicates were included, except male resistant 25 (n = 3) and female resistant 300 (n = 2). Pacific pre-adult lice of both sexes were exposed to a dilution series: 0 (control), 25, 50 parts per billion EMB.
2014-11-17 | E-GEOD-56024 | biostudies-arrayexpress
Project description:To investigate whether lncRNAs are involved in intergenerational inheritance of obesity and obesity-induced decline in fertility, we divided mice into obesity (F0 mice fed a high-fat diet, F0-HFD) and non-obese (F0 mice fed normal chow, F0-NC) model groups and their male offspring (F1-HFD and F1-NC, respectively). We examined the differences in the expression levels of lncRNAs and mRNAs in the F0-HFD/F0-normal and F1-HFD/F1-normal groups. The results revealed similar expression patterns in the F1-HFD/F0-HFD groups at both the lncRNA and mRNA levels. The maximum difference in the lncRNA expression was observed between the F0-HFD and F0-NC groups. The differentially expressed lncRNA targets and mRNAs identified in our study are mainly involved in GnRH signalling pathway, metabolic process, and Hippo signalling pathway; similarly expressed lncRNAs and mRNAs in F1-HFD/F0-HFD are closely linked with G-protein coupled receptor signalling pathway, pancreatic polypeptide receptor activity, and lysine biosynthesis, which may play an important role in the molecular mechanism of intergenerational inheritance of obesity. Furthermore, potential genes that might play important roles in the pathogenesis of obesity-related low fertility were revealed by lncRNA-and mRNA-interaction studies based on the microarray expression profiles. In conclusion, we found that lncRNA could be involved in obesity-induced infertility by expressing abnormalities, which could act as genetic vectors of paternal inheritance of obesity.
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