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Series GSE6009 Query DataSets for GSE6009
Status Public on Oct 10, 2007
Title Long Serial Analysis of Gene Expression (LongSAGE) of Chinook salmon (Oncorhynchus tshawytscha) brain tissue.
Organism Oncorhynchus tshawytscha
Experiment type Expression profiling by SAGE
Summary Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Populations return to freshwater for spawning at many different times of year, resulting in segregated populations that may use differing molecular pathways for these large behavioral and physiological differences. Using a population of Chinook from California’s Central Valley, we sought to generate novel expressed sequences using Long Serial Analysis of Gene Expression (LongSAGE). We constructed three LongSAGE libraries from brains of samples caught in the spring and fall in freshwater and from the ocean. Using cDNA libraries from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), we were able to assign 59% of putatively differentially expressed tags to genes. Additionally, we tested the expression levels of seven genes, indicated by LongSAGE to be putatively differentially expressed between the fall and spring, and found none significantly differentially expressed. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future research on gene expression differences between Chinook salmon of different populations, as well as underlying mechanisms of differing physiology and behavior.
Keywords: seasonal difference
Overall design Single individuals were used to construct each LongSAGE library. The fall, spring and ocean samples were then compared between each other and examined for differences in the number of tags observed.
Contributor(s) Bernier JC, Birkeland SR, Cipriano MJ, McArthur AG, Banks MA
Citation J C Bernier, S R Birkeland, M J Cipriano, Andrew G McArthur, M A Banks. Differential gene expression between fall and spring run Chinook salmon (Oncorhynchus tshawytscha) assessed by long serial analysis of gene expression (LongSAGE). Transactions of the American Fisheries Society. 2008;137:1378-1388.
Submission date Oct 10, 2006
Last update date Mar 16, 2012
Contact name Jeremiah Bernier
Phone (541) 867-0420
Organization name Hatfield Marine Science Center, Oregon State University
Department Fisheries and Wildlife
Lab Marine Fisheries Genetic Laboratory
Street address 2030 SE Marine Science Drive
City Newport
State/province OR
ZIP/Postal code 97365
Country USA
Platforms (1)
GPL4407 SAGE:17:NlaIII:Oncorhynchus tshawytscha
Samples (3)
GSM139480 whole brain_chinook_fall
GSM139481 whole brain_chinook_spring
GSM139482 whole brain_chinook_ocean
BioProject PRJNA97805

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