Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657498 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12471400_1.fastq.gz | Fastqsanger.gz | |||
| SRR12471400_2.fastq.gz | Fastqsanger.gz | |||
| SRR12471500_1.fastq.gz | Fastqsanger.gz | |||
| SRR12471500_2.fastq.gz | Fastqsanger.gz | |||
| SRR12471401_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
2017-02-21 | GSE95082 | GEO
Project description:Rainbow darter (Etheostoma caeruleum) are a small benthic fish found in North America. This species is sensitive to sewage effluent in the environment, showing the presence of intersex in up to 80% of males in near-field areas in the Grand River, ON. To learn more about the molecular events associated with intersex, we developed a customized oligonucleotide microarray (4x180K) with next generation sequencing (454 Roche) to characterize molecular responses in the gonad. Transcriptomics was performed on both males and females from both a reference site and a polluted site. Males with and without intersex from the polluted site were compared to the control males. Rainbow darter were sampled from from the Grand River in May 2011. Fish were selected according to the location, gonad maturity, and intersex index. Reference fish were taken from the upstream to the urban area; exposed fish were taken from downstream of from Kitchener MWWE treatment plant.
2014-05-22 | E-GEOD-57394 | biostudies-arrayexpress
Project description:Rainbow darter (Etheostoma caeruleum) are a small benthic fish found in North America. This species is sensitive to sewage effluent in the environment, showing the presence of intersex in up to 80% of males in near-field areas in the Grand River, ON. To learn more about the molecular events associated with intersex, we developed a customized oligonucleotide microarray (4x180K) with next generation sequencing (454 Roche) to characterize molecular responses in the gonad. Transcriptomics was performed on both males and females from both a reference site and a polluted site. Males with and without intersex from the polluted site were compared to the control males.
2014-05-22 | GSE57394 | GEO
Project description:We have been studying intersex in male rainbow darter (Etheostoma caeruleum) associated with exposure to sewage effluents. To understand changes in the gene transcriptome associated with intersex it was necessary to have a better understanding of normal annual changes in the transcriptome. The goal of this research is to identify patterns of gene expression associated with the different stages of gonad development during the annual cycle. The studies of molecular pathways involve in ovarian or testis development has been poorly studied. While most studies focus on female ovarian changes, there is a gap in understanding testis development. A customized second generation microarray for rainbow darter (8x15k) was used to identify patterns of gene expression -in terms of mRNA abundance- in male rainbow darter gonads during an annual cycle. Rainbow darter males were collected on field work surveys in May (spawning), August (post-spawning), and October (recrudescence) 2011, and January (developing) and March (pre-spawning) 2012, using a back pack electrofisher from a clean area at the Grand River, ON, Canada.
2014-05-22 | E-GEOD-57865 | biostudies-arrayexpress
Project description:We have been studying intersex in male rainbow darter (Etheostoma caeruleum) associated with exposure to sewage effluents. To understand changes in the gene transcriptome associated with intersex it was necessary to have a better understanding of normal annual changes in the transcriptome. The goal of this research is to identify patterns of gene expression associated with the different stages of gonad development during the annual cycle. The studies of molecular pathways involve in ovarian or testis development has been poorly studied. While most studies focus on female ovarian changes, there is a gap in understanding testis development. A customized second generation microarray for rainbow darter (8x15k) was used to identify patterns of gene expression -in terms of mRNA abundance- in male rainbow darter gonads during an annual cycle.
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Project description:The federally endangered Okaloosa darter (Etheostoma okaloosae) is found almost exclusively on the Eglin Air Force Base in the Choctawhatchee Bay watershed of Florida. Portions of this limited habitat are threatened with erosion of soils, altered hydrology, and impaired water quality. One stream reach in particular, East Turkey Creek, has demonstrated potential water quality problems including poor invertebrate bioassessment scores (IBI), uncharacteristically high conductivity values, and low numbers of Okaloosa darters. General water quality (dissolved oxygen, specific conductance, pH, temperature, and relative turbidity and primary productivity) was characterized in both the potentially impacted East Turkey Creek and a reference stream (Long Creek). Water quality was assessed during a 30 day exposure using passive samplers for both non-polar and polar effluent parameters. Metal loading in the system was assessed via fish tissue burdens in resident Pteronotropis hypseleotris. Additionally, microarray analysis was performed on gonad and liver tissue from fathead minnows, Pimephales promelas, after 48-h exposures to water collected from the two creeks and brought into the laboratory. Gene expression changes were evident at the site below the influence of a wastewater spray field sited along East Turkey Creek, suggesting that anthropogenic compounds in the effluent waters may have affected both liver and testis function and could be related to account the general decrease in populations of the Okaloosa darter.
2010-08-11 | GSE23521 | GEO
Project description:The federally endangered Okaloosa darter (Etheostoma okaloosae) is found almost exclusively on the Eglin Air Force Base in the Choctawhatchee Bay watershed of Florida. Portions of this limited habitat are threatened with erosion of soils, altered hydrology, and impaired water quality. One stream reach in particular, East Turkey Creek, has demonstrated potential water quality problems including poor invertebrate bioassessment scores (IBI), uncharacteristically high conductivity values, and low numbers of Okaloosa darters. General water quality (dissolved oxygen, specific conductance, pH, temperature, and relative turbidity and primary productivity) was characterized in both the potentially impacted East Turkey Creek and a reference stream (Long Creek). Water quality was assessed during a 30 day exposure using passive samplers for both non-polar and polar effluent parameters. Metal loading in the system was assessed via fish tissue burdens in resident Pteronotropis hypseleotris. Additionally, microarray analysis was performed on gonad and liver tissue from fathead minnows, Pimephales promelas, after 48-h exposures to water collected from the two creeks and brought into the laboratory. Gene expression changes were evident at the site below the influence of a wastewater spray field sited along East Turkey Creek, suggesting that anthropogenic compounds in the effluent waters may have affected both liver and testis function and could be related to account the general decrease in populations of the Okaloosa darter. Array hybridizations were performed using a single color design. Four biological replicates consisting of four different individuals were analyzed for each of the treatments (University of Florida control, and each of five sites). Site C was left out of subsequent analysis for publication, due to poor characterization of the site. Two Samples were left out of the normalization/analysis due to QC failure. Therefore, there are only 3 replicates of the "testis, site A water, exposed 48 h." and "liver, site E water, exposed 48 h." groups.
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