Pacific salmon gill samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Oncorhynchus nerka
SUBMITTER: 
Paul Pavlidis
PROVIDER: E-GEOD-22179 | ArrayExpress | 2010-12-31
SECONDARY ACCESSION(S): GSE22179PRJNA127557
REPOSITORIES: GEO, ArrayExpress
Dataset's files
primary
| Action | |||
|---|---|---|---|
| E-GEOD-22179.README.txt | Txt | ||
| E-GEOD-22179.idf.txt | Idf | ||
| E-GEOD-22179.processed.1.zip | Processed | ||
| E-GEOD-22179.raw.1.zip | Raw | ||
| E-GEOD-22179.raw.2.zip | Raw |
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Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.
2010-12-31 | E-GEOD-22177 | ArrayExpress
Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series is of gill expression profiles from the study of fish sampled and tagged in the ocean and tracked as they entered the river system and swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.
2010-12-31 | E-GEOD-22171 | ArrayExpress
Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish at the Weaver creek spawning grounds, and were observed for pre-spawning mortality or successful spawning. Weaver creek sockeye salmon (a late-run stock) spawn in an artificial spawning channel which has a controlled entrance and no exit, situated 100 km from the ocan. Females were dip-netted out of the entrance of the spawning channel, and placed into a sampling trough with flowing ambient water for the gill biopsy procedure and tagged with Petersen discs and returned to the spawning channel. Moribund fish were recovered daily and their gonads examined to assess whether they had spawned or not. Gene expression was assayed on the GRASP salmonid 32K cDNA microarray.
2010-12-31 | E-GEOD-22347 | ArrayExpress
Project description:We collected sockeye salmon from the Fraser River, British Columbia, and held them at ecologically relevant temperatures (14C and 19C) determine the effect of elevated water temperature on cellular processes in non-lethally sampled gill tissue and blood plasma over a period of seven days that represents a significant portion of their upstream migration. Time-matched fish that died prematurely over the course of the holding study were also sampled for gill tissue and the transcriptomic responses in moribund fish were compared with surviving fish. This is the first study to experimentally examine transcriptomic responses to high water temperature and premature mortality in wild-caught Pacific salmon and the results will help in understanding some of the cellular mechanisms involved in large-scale migration mortality in Pacific salmon during warm water periods and for predicting or understanding causes of mortality in naturally senescing adult Pacific salmon. Forty samples were analyzed on forty two-channel microarrays, using a common reference design, with multiple biological replicates for each temperature condition. Fish were further classified into survivor and moribund based on their status after 7 days in captivity.
2012-05-30 | E-GEOD-33586 | ArrayExpress
Project description:a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities. Fish were captured fish at two marine sampling sites, one within Johnstone Strait (JS), BC. Canada and one within Juan De Fuca Strait (JDFS), BC Canada. Ocean sites were contrasted to fish sampled within the Fraser River at Whonnock (W), BC, Canada. Gill and liver tissues were dissected at each of these sites. Non-lethal biopsy sampling was performed on migrating sockeye salmon intercepted within the Fraser River at Mission, BC, Canada and genetically-based stock ID was used to determine the stock-specific spawning grounds for each fish, giving an intended end-point of migration for each of the stocks investigated in this study.Gene expression levels were determined by comparing the amount of mRNA transcript in the experimental samples relative to a reference sample. A total of 123 microarrays were used to generate the dataset, corresponding to individual hybridizations of both gill and liver samples collected from JS (gill n=14; liver n=15), JDFS (gill n=15; liver n=13), W (gill n=11; liver n=10), and biopsy sampled gill tissue collected at Mission (n=45).Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The reference contained the combined aRNA of all individuals used in the experiment, excluding bioposy sampled fish. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, and no dye swaps were perfromed.
2011-06-12 | E-GEOD-22346 | ArrayExpress
Project description:A large-scale functional genomics study revealed shifting energy generating processes in white muscle during the final 1,300 km migration of wild sockeye salmon to their spawning grounds in the Fraser River, British Columbia. In 2006, Lower Adams stock sockeye salmon ceased feeding after passing the Queen Charlotte Islands, 850 km from the Fraser River. Enhanced protein turnover and reduced transcription of actin, muscle contractile and heme-related proteins were early starvation responses in saltwater. Arrival to the estuarine environment triggered massive protein turnover through induction of proteasoma and lysosomal proteolysis and protein biosynthesis, and a shift from anaerobic glycolysis to oxidative phosphorylation. Response to entry into freshwater was modest, with up-regulation of heat shock proteins and nitric oxide biosynthesis. High river temperatures resulted in a strong defense/immune response and high mortalities in 50% of fish. Arrival to the spawning grounds triggered further up-regulation of oxidative phosphorylation and proteolysis, down-regulation of protein biosynthesis and helicase activity, and continued down-regulation of muscle proteins and most glycolytic enzymes. However, sharp up-regulation of PFK-I indicated induction of glycolytic potential at the spawning grounds. The identification of potential environmental cues triggering genome-wide transcriptional shifts in white muscle associated with migration and the strong activation of proteasomal proteolysis were both novel findings. Keywords: Functional genomics study on wild-caught fish The experiment was based on expression profiles of white muscle tissue collected from wild migrating adult sockeye salmon during their return spawning migration back to the Fraser River. Fish were collected from seven sites along the final 1,300 km migration path, and white muscle samples were quickly frozen in liquid nitrogen upon capture. Marine sampling sites included (from north to south) the Queen Charlotte Islands (QCI), Johnstone Strait (JS), Juan de Fuca Strait (JDFS), and the Strait of Georgia (SOG). Freshwater sampling sites included Whonnock (W), Savona (SV) and the Lower Adams Spawning Grounds. Genetically-based stock ID was used to identify the natal sites of fish collected from the wild. The experiment was designed to profile the transcriptional shifts associated with migration of the Adams River stock complex. The total experiment included 80 microarray slides, with a minimum biological replicate size per site of 6 (SV), and maximum of 18 (JS) (see supplemental table for details). Additional intra-site variables, which could only be addressed in some sites, included sex (female biased) and river entry timing (for JS, JDFS and W sites; identified through radio-tracking of marine collected fish). Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The experiment was based on a reference design, with the reference containing the combined aRNA of all individuals used in the experiment. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, with no dye flips included. A single technical replicate of one SV fish (replicate 5) was included in the experimental design. This experiment is part of a larger white muscle experiment containing additional sockeye salmon stocks.
2010-05-15 | E-GEOD-13657 | ArrayExpress
Project description:Characterizing a common cellular stress response (CSR) to high water temperature across species and populations is necessary for identifying the capacity of Pacific salmon (Oncorhynchus spp.) to persist in current and future climate warming scenarios, especially for populations at the southern periphery of their species' distributions. In this study, populations of wild adult pink (O. gorbuscha) and sockeye (O. nerka) salmon from the Fraser River, British Columbia, Canada, were experimentally treated to an ecologically relevant 'cool' or 'warm' water temperature to uncover common transcriptomic responses to elevated water temperature. Ninety-eight samples from three separate temperature exposure studies were analyzed on ninety-eight microarrays, using a common reference design, with multiple biological replicates for each temperature condition for each year of the experiment.
2013-11-01 | E-GEOD-42556 | ArrayExpress
Project description:Characterizing a common cellular stress response (CSR) to high water temperature across species and populations is necessary for identifying the capacity of Pacific salmon (Oncorhynchus spp.) to persist in current and future climate warming scenarios, especially for populations at the southern periphery of their species' distributions. In this study, populations of wild adult pink (O. gorbuscha) and sockeye (O. nerka) salmon from the Fraser River, British Columbia, Canada, were experimentally treated to an ecologically relevant 'cool' or 'warm' water temperature to uncover common transcriptomic responses to elevated water temperature. Ninety-eight samples from three separate temperature exposure studies were analyzed on ninety-eight microarrays, using a common reference design, with multiple biological replicates for each temperature condition for each year of the experiment.
2013-11-01 | E-GEOD-42555 | ArrayExpress
Project description:Pacific salmon gill samples: fate tracking in river
| PRJNA129193 | ENA
Project description:Exposure to environmental contaminants like nonylphenol can disrupt smolt development and may be a contributing factor in salmon population declines. We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of Atlantic salmon smolts treated with nonylphenol compared to control smolts. Nonylphenol treatment was confirmed using physiological assays: nonylphenol-treatment significantly decreased gill Na+,K+-ATPase activity and plasma cortisol and T3 levels. Microarray analyses were used to compare expression in nonylphenol-injected fish with expression in vehicle-injected fish: eight arrays each for liver, gill, olfactory rosettes, hypothalamus, and pituitary tissues. Total RNA was isolated from the tissues of eight nonylphenol-injected fish (six males and two females) and eight vehicle-injected fish (two males and six females) and reverse transcribed separately (not pooled); each slide represents a biological replicate. For each tissue, the eight arrays were balanced for dye: nonylphenol-injected fish were labeled with Alexa Fluor 555 and vehicle-injected fish were labeled with Alexa Fluor 647 on four slides, nonylphenol-injected fish were labeled with Alexa Fluor 647 and vehicle-injected fish were labeled with Alexa Fluor 555 on four slides. Liver, gill, hypothalamus, pituitary, and olfactory rosette tissues were analyzed separately.
2012-06-03 | E-GEOD-33715 | ArrayExpress