Genomics

Dataset Information

0

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [liver]


ABSTRACT: There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation. Overall design: A total of 735 microarrays were run over 284 Coho salmon. 1 experimental sample and 1 pooled reference sample per microarray. These samples were comprised of four salmon tissues (brain, gill, liver and muscle) and represented six life stages, two of which occurred in freshwater (parr, smolt) and four postsmolt which occurred in saltwater (spring, summer, fall, winter). All four tissues were run for 48 samples (17%) and brain, liver and muscle were examined for 148 (52%) of the samples. The lack of gill tissue for some samples was due to the fact that the gill slides were split between Coho salmon (Oncorhynchus kisutch) and Sockeye salmon (Oncorhynchus nerka).

INSTRUMENT(S): Agilent-025055 Koop Lab Salmonid 44k

ORGANISM(S): Oncorhynchus kisutch  

SUBMITTER: Shaorong Li  

PROVIDER: GSE123307 | GEO | 2019-12-03

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE123307_processed_data_liver_withallcontrols.txt.gz Txt
GSE123307_raw_data_liver.tar.gz Other
Items per page:
1 - 2 of 2

Similar Datasets

2019-12-03 | GSE123305 | GEO
2019-12-03 | GSE123304 | GEO
2019-12-03 | GSE123306 | GEO
2019-01-01 | S-EPMC6788492 | BioStudies
2020-01-01 | S-EPMC7746168 | BioStudies
2014-06-20 | E-GEOD-58670 | ArrayExpress
2017-01-01 | S-EPMC5292104 | BioStudies
2010-06-01 | E-MEXP-2210 | BioStudies
2012-08-20 | E-GEOD-33711 | BioStudies
2007-10-10 | GSE6009 | GEO