Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552428 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9639540_1.fastq.gz | Fastqsanger.gz | |||
| SRR9639540_2.fastq.gz | Fastqsanger.gz | |||
| SRR9639550_1.fastq.gz | Fastqsanger.gz | |||
| SRR9639550_2.fastq.gz | Fastqsanger.gz | |||
| SRR9639560_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Recirculation systems (RAS), which reduce water consumption and improve pathogen control are increasingly used in Atlantic salmon aquaculture. Performance and adaptation of fish to new farming environment is actively investigated. Here, responses to crowding stress were compared in salmon reared in two systems (RAS with brackish water and flowthrough with full salinity water) at low and high density.
2021-04-27 | GSE173229 | GEO
Project description:Rearing density and dietary yeast on microbiota of tilapia
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Project description:An unintended consequence of fish farming is the production of an environment which may be conducive for the evolution of virulence for pathogens interacting with the host in production. Rearing conditions used in salmon aquaculture such as high densities, compressed rearing cycles, limited genetic diversity of broodstock as well as practices applied to control infectious disease, may all lead to increased selection pressures for the evolution of virulence of pathogens. These selection pressures may also be occurring without the balancing of negative fitness costs of virulence due to a constant supply of naïve hosts entering the system every 18-24 months. Changes in virulence of Canadian Lepeophtheirus salmonis populations have not yet been assessed, despite having been identified as a crucial knowledge gap to understand the interactions between farmed and wild hosts as well as the impact of increased disease prevalence at sites which may harbour highly virulent strains. We developed a virulence challenge model by rearing lice originating from wild and farm sources for 6 generations and compared differences in virulence on their host, testing the hypothesis that lice originating from farms were more virulent than those from wild sources. RNA sequencing was completed for copepodid, chalimus II and adult stages of the louse as well as their respective attachment sites on the host to determine responses at the host-parasite interface. We describe the first instance of elevated lesion severity for host Atlantic salmon when infected with farm-sourced lice compared to their wild counterparts. However, this increase did not appear to translate to meaningful differences in host growth rates (e.g. change in lengths or weights). Approximately 900 transcripts had differential expression for at least one life stage between wild and farm sources of lice. Many of these transcripts had functions related to chitin- and heme-binding, serine-endopeptidase, metallo-endopeptidase, and trypsin-like activities.
2025-04-18 | GSE295072 | GEO
Project description:Farmed salmon individuals from AquaGen AS was sampled and hindgut tissue was taken for RNAseq
2022-10-01 | E-MTAB-8308 | biostudies-arrayexpress
Project description:Here we used RNAseq in juvenile pink salmon (Oncorhynchus gorbuscha) exposed to crude oil at different concetrations to identify molecular changes associated with cardiac defects.
2018-08-10 | GSE102654 | GEO
Project description:Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 4 mo old rhesus macaques subject to maternal rearing, peer rearing, or surrogate peer rearing. The primary research question is whether gene expression differs as a function of early rearing conditions.
2012-12-03 | GSE35850 | 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