Transcriptomics,Genomics

Dataset Information

35

Spatail gradient approach application in assessing changes in the rainbow darter (Etheostome caeruleum) liver transcriptome in the Grand River, Ontario


ABSTRACT: In this study, adult male rainbow darter (Etheostoma caeruleum) were collected from nine sites located at different distances from two wastewater treatment plants (WWTPs) in the Grand River, Ontario, Canada. The goal of this project was to see if the liver transcriptome of fish residing downstream of the two WWTPs differs from the non-exposed fish. Further, this research was also addressing the affects of differnent reference site selection on gene expression patterns, and their subsequent interpretation.The RNA from male rainbow darter was exctracted from liver tissue and used for further gene expression analysis. Overall design: Fish collections were conducted in the fall of 2013 (Oct-Nov). Experimental design included 9 sites: 3 reference sites (US1, US2 and US3), located upstream, in the non-urbanized area; an exposure site located downstream of Wateloo WWTP (DSW), an intermidiate site (INT), that was located in the urbanized area between the two WWTPs, a second exposure site, downstram of Kitchener WWTP (DSK1); there were also three downstream sites (DSK2, DSK3 and DSK4) whre revovery was possible. There were 63 samples analyzed, 7 samples per site. There was a total of 63 microarrays processed.

INSTRUMENT(S): Agilent-042064 UNBSJ rainbow darter 15k v2.0

SUBMITTER: Patricija Marjan  

PROVIDER: GSE95082 | GEO | 2017-02-21

SECONDARY ACCESSION(S): PRJNA376010

REPOSITORIES: GEO

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Publications

How Does Reference Site Selection Influence Interpretation of Omics Data?: Evaluating Liver Transcriptome Responses in Male Rainbow Darter (Etheostoma caeruleum) across an Urban Environment.

Marjan Patricija P   Bragg Leslie M LM   MacLatchy Deborah L DL   Servos Mark R MR   Martyniuk Cristopher J CJ  

Environmental science & technology 20170517 11


Studies quantifying the influence of reference site selection on transcriptomic profiles in aquatic organisms exposed to complex mixtures are lacking in the literature, despite the significant implications of such research for the interpretation of omics data sets. We measured hepatic transcriptomic responses in fish across an urban environment in the central Grand River watershed (Ontario, Canada). Adult male rainbow darter (RBD) (Etheostoma caeruleum) were collected from nine sites at varying  ...[more]

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