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Dose-dependent hepatic transcriptional responses in Atlantic salmon (Salmo salar) exposed to sublethal doses of gamma radiation

ABSTRACT: To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 15 mGy, 70 mGy and 280 mGy external gamma radiation. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR.

ORGANISM(S): Salmo salar salmonid fish

PROVIDER: GSE59035 | GEO | 2014/07/03

SECONDARY ACCESSION(S): PRJNA254169

REPOSITORIES: GEO

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Dose-dependent hepatic transcriptional responses in Atlantic salmon (Salmo salar) exposed to sublethal doses of gamma radiation

Project description:To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 15 mGy, 70 mGy and 280 mGy external gamma radiation. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR. Juvenile Atlantic salmon were exposed to external gamma radiation emitted from a cobalt-60 source for 48 h. Liver were sampled and used for gene expression analysis.

2014-07-03 | E-GEOD-59035 | biostudies-arrayexpress

Combined hepatic transcriptional effects of gamma radiation and depleted uranium on Atlantic salmon (Salmo salar)

Project description:To study the short-term hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 70 mGy external gamma radiation, 0.25 mg/L depleted uranium and combination of these two. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was used to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR.

2015-10-14 | GSE74012 | GEO

Hepatic transcriptomic profiling reveals early toxicological mechanisms of uranium in Atlantic salmon (Salmo salar)

Project description:To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 0.25 mg/L, 0.5 mg/L and 1.0 mg/L depleted uranium. A combination of high density (60 k) custom oligonucleotide salmonid miacroarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR. Juvenile Atlantic salmon were exposed to waterborne depleted uranium for 48 h. Liver were samples and used for gene expression analysis.

2014-06-26 | E-GEOD-58824 | biostudies-arrayexpress

Hepatic transcriptomic profiling reveals early toxicological mechanisms of uranium in Atlantic salmon (Salmo salar)

2014-06-26 | GSE58824 | GEO

Ethynylestradiol (EE2) effect on global gene expression in primary rainbow trout (Oncorhynchus mykiss) hepatocytes

Project description:To study short term (48h) hepatic transcriptional changes and identify potential modes of action in primary rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to 0.03, 0.3, 3 and 30nM EE2. The transcriptional gene expression analysis involved a high density (60k) custom designed oligonucleotide salmonid microarray in combination with quantitative real-time polymerase chain reaction (qPCR). Differently expressed genes (DEGs) were obtained after application of a one-way analysis of variance (ANOVA) and Tukey posthoc test. Enrichment analysis was performed based on Gene Ontology (GO) to determine the biological roles of the DEGs. The obtained DEGs were further mapped against mammalian orthologs. The successfully mapped DEGs were further subjected to a gene network analysis based on well-curated mammalian protein -protein interactions, followed by a canonical and toxicity pathway analysis. The pathways and network analysis were performed in order to link DEGs to specific and toxicological/biological functions. Isolated primary rainbow trout hepatocytes were exposed to 0.03-30nM ethynylestradiol for 48h. The cells were sampled and used for gene expression analysis. A total of 4 biological replicates were analyzed for each concentration, including solvent (DMSO) control.

2015-10-31 | E-GEOD-68335 | biostudies-arrayexpress

Ethynylestradiol (EE2) effect on global gene expression in primary rainbow trout (Oncorhynchus mykiss) hepatocytes

2015-10-31 | GSE68335 | GEO

Bone collagen from Pacific salmonid species contains differences allowing for peptide mass fingerprinting for easy identification

Project description:MS/MS spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen.

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Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics

Project description:Comparison of two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar)

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Transcriptional changes in Atlantic salmon (Salmo salar) after embryonic exposure to road salt (NaCl)

Project description:The present study aimed to identify the persistent molecular changes occurring in Atlantic Salmon salmon (Salmo salar) eggs after 24h exposure to high concentrations (5000 mg/L) of road salt at fertilization. Atlantic Salmon (Salmo salar) eggs after fertilization were exposed to high concentrations (5000 mg/L) of road salt for 24 h and used for gene expression analysis.

2015-08-05 | E-GEOD-71714 | biostudies-arrayexpress

Transcriptional changes in Atlantic salmon (Salmo salar) after embryonic exposure to road salt (NaCl)

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