Ontology highlight
ABSTRACT:
PROVIDER: PRJNA539967 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8979740.fastq.gz | Fastqsanger.gz | |||
| SRR8979741.fastq.gz | Fastqsanger.gz | |||
| SRR8979732.fastq.gz | Fastqsanger.gz | |||
| SRR8979742.fastq.gz | Fastqsanger.gz | |||
| SRR8979733.fastq.gz | Fastqsanger.gz |
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Project description:This project utilized oligonucleotide microarrays to examine gene expression patterns in adult male fathead minnows (Pimephales promelas) exposed to a common nanomaterial, titanium dioxide (TiO2, stearate-coated particles, MT-100TV®). We exposed adult male fathead minnows for 96 hr to three doses (0, 1, and 10 mg/L nominal) of TiO2 under static renewal conditions. TiO2 is stearate coated, 15 nm particle size.
2010-12-22 | GSE17902 | GEO
Project description:Here, we employed integrated chemical and biological analyses to determine how environmental mixtures affected biological responses in watersheds with different landuse. Adult male fathead minnows (Pimephales promelas) were exposed to water from different locations within the Shenandoah River watershed (VA, USA) in 2014, 2015, and 2016. The exposure locations were chosen to capture unique landuse in surrounding watersheds, including agricultural, municipal, mixed-use, and forested sites. Gene expression profiles were measured in livers of male fish exposed for 7 days using Agilent 60K custom FHM microarrays.
2019-06-01 | GSE111966 | GEO
Project description:Here, we employed integrated chemical and biological analyses to determine how environmental mixtures affected biological responses in watersheds with different landuse. Adult male fathead minnows (Pimephales promelas) were exposed to water from different locations within the Shenandoah River watershed (VA, USA) in 2014, 2015, and 2016. The exposure locations were chosen to capture unique landuse in surrounding watersheds, including agricultural, municipal, mixed-use, and forested sites. Gene expression profiles were measured in livers of male fish exposed for 7 days using Agilent 60K custom FHM microarrays.
2019-06-01 | GSE111965 | GEO
Project description:Here, we employed integrated chemical and biological analyses to determine how environmental mixtures affected biological responses in watersheds with different landuse. Adult male fathead minnows (Pimephales promelas) were exposed to water from different locations within the Shenandoah River watershed (VA, USA) in 2014, 2015, and 2016. The exposure locations were chosen to capture unique landuse in surrounding watersheds, including agricultural, municipal, mixed-use, and forested sites. Gene expression profiles were measured in livers of male fish exposed for 7 days using Agilent 60K custom FHM microarrays.
2019-06-01 | GSE122978 | GEO
Project description:This project utilized oligonucleotide microarrays to examine gene expression patterns in adult male fathead minnows (Pimephales promelas) exposed to a common nanomaterial, titanium dioxide (TiO2, stearate-coated particles, MT-100TV®). We exposed adult male fathead minnows for 96 hr to three doses (0, 1, and 10 mg/L nominal) of TiO2 under static renewal conditions. TiO2 is stearate coated, 15 nm particle size. Three-condition experiment: high dose, controls (untreated, low dose). Three tissues: liver, gill, brain. Biological replicates: 4 control replicates, 4 low dose, 4 high dose for gill and liver. One array for brain control and low dose; and 2 arrays for brain high dose. Contributor: Johnson & Johnson Worldwide Envrionmental
2010-12-22 | E-GEOD-17902 | biostudies-arrayexpress
Project description:Aromatase, a member of the cytochrome P450 superfamily, is a key enzyme in estrogen synthesis and is responsible for the aromatization of androgens into estrogens. Here, we used an integrated approach to better understand the effects of aromatase inhibition as well as the mechanisms involved in the adaptation and recovery process. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase. We used transcriptomics, metabolomics, and network inference to understand changes and infer connections at the transcript and metabolite level in the ovary. Other apical endpoints such as plasma estradiol, testosterone, and vitellogenin levels were also measured. An integrated analysis of the data revealed changes in gene expression consistent with increased testosterone. Metabolites such as glycogen and taurine were strongly correlated with increased testosterone levels. Comparison of in vivo and ex vivo data suggested the accumulation of steroidogenic enzymes, including aromatase, as a mechanism to compensate for aromatase inhibition. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase.
2013-11-01 | E-GEOD-51961 | biostudies-arrayexpress
Project description:Production, usage and disposal of the munitions constituent (MC) cyclotrimethylenetrinitramine (RDX) has led to environmental releases on military facilities. The chemical attributes of RDX are conducive for leaching to surface water which may put aquatic organisms at risk of exposure. Because RDX has been observed to cause aberrant neuromuscular effects across a wide range of animal phyla, we assessed the effects of RDX on central nervous system (CNS) function in the representative aquatic ecotoxicological model species, fathead minnow (Pimephales promelas). A brain-tissue based cDNA library enriched for transcripts differentially expressed in response to RDX exposure was developed for fathead minnow and was transitioned to custom cDNA-based microarrays. All 4,128 cDNAs were sequenced, quality filtered and assembled yielding 3,018 unique sequences and 945 significant blastx matches (E ≤ 10-5). Bioassays were conducted exposing fathead minnows to RDX at 0.625, 1.25, 2.5, 5, 10 mg/L or an acetone-spike control for 10d. Overt toxicity of RDX in fathead minnow occurred only at the highest exposure concentration resulting in 50% mortality. Conversely, Bayesian analysis of microarray data indicated significant changes in transcript expression in fathead minnow brain tissue at RDX concentrations as low as 0.625 mg/L. In total, 154 microarray targets representing 44 unique transcript identities were differentially expressed in RDX exposures, the majority of which were validated by RT-qPCR. Investigation of molecular pathways, gene ontology and individual gene functions indicated that RDX exposures affected metabolic processes involved in: oxygen transport, neurological function, calcium binding / signaling, energy metabolism, cell cycle / cell proliferation, oxidative stress and ubiquitination. In total, our study indicated that RDX exposure affected molecular processes critical to CNS function in fathead minnow. 10 Day RDX Exposure, Brain Tissue Investigation: Sub-adult fathead minnows were exposed to RDX in a 10d dose-series experiment (0.625, 1.25, 2.5, 5.0, or 10 mg/L RDX) which included an acetone-spike control (1% acetone). Each experimental treatment included 8 replicate fish (48 total fish) and endpoints included mortality, total weight and neurotoxicogenomics. The 1.25mg/L dose was not included in the microarray experiment. Please see attached PDF file for detailed 'Balanced, Interwoven Loop Design'.
2010-07-30 | E-GEOD-21153 | biostudies-arrayexpress
Project description:Metformin, along with its biotransformation product guanylurea, are commonly observed in municipal wastewaters and subsequent surface waters. Previous studies in fish have identified metformin as a potential endocrine active compound but there are inconsistencies in the literature with regard to effects. To further investigate the potential reproductive toxicity of metformin and guanylurea to fish, a series of experiments were performed with reproductively mature fathead minnows (Pimephales promelas). First, explants of mature fathead minnow ovary tissue were exposed to 0.001-100 µM metformin or guanylurea to investigate whether they can directly perturb steroidogenesis. Second, spawning pairs of fathead minnows were exposed to metformin (0.41, 4.1, 41 µg/L) or guanylurea (1.0, 10, 100 µg/L) for 23 d to assess impacts on reproduction. Lastly, male fathead minnows were exposed to 41 µg/L metformin, 100 µg/L guanylurea, or a mixture of both compounds, with samples collected over a 96 h time course to investigate potential impacts to the hepatic transcriptome or metabolome. Neither metformin or guanylurea effected estradiol or testosterone by ovary tissue exposed in vitro. In the 23 d exposure, neither compound significantly impacted transcription of endocrine-related genes in male liver or gonad, circulating steroid concentrations in male or female fish, or fecundity of spawning pairs. In the 96 h time course, 100 µg guanylurea/L elicited more differential gene expression than 41 µg metformin/L , and showed the greatest impacts after 96 h. A number of DEGs up-regulated after 24 h were subsequently down-regulated after 96 h, demonstrating time-dependent impacts of guanylurea on the liver. Overall, metformin and guanylurea did not elicit effects consistent with reproductive toxicity in adult fathead minnows at environmentally relevant concentrations. Where effects were identified using ‘omics approaches, guanylurea induced greater impacts than metformin.
2023-03-03 | GSE198081 | GEO
Project description:This study aimed to evaluate the utility of microarrays as a biomonitoring tool in field studies. A 15,000-oligonucleotide microarray was used to measure the hepatic gene expression of fathead minnows (Pimephales promelas) caged in four Nebraska, USA watersheds - the Niobrara and Dismal Rivers (low-impact agricultural sites) and the Platte and Elkhorn Rivers (high-impact agricultural sites). Gene expression profiles were site specific and fish from the low- and high-impact sites aggregated into distinct groups. Over 1500 genes were differentially regulated between fish from the low- and high-impact sites. Many gene expression differences (1218) were also noted when the Platte and Elkhorn minnows were compared to one another and Platte fish experienced a higher degree of transcript alterations than Elkhorn fish. These findings indicate that there are differences between the low-impact and high-impact sites, as well as between the high-impact sites. Historical water quality data supports these results as only trace levels of agrichemicals have been detected at the low-impact sites, while substantial levels of agrichemicals have been reported at the high-impact sites with agrichemical loads at the Platte generally exceeding those at the Elkhorn. Overall, this study demonstrates that microarrays can be utilized to discriminate sites with different contaminant loads from one another. A 15,000-oligonucleotide microarray was used to measure the hepatic gene expression of fathead minnows (Pimephales promelas) caged in four Nebraska, USA watersheds - the Niobrara and Dismal Rivers (low-impact agricultural sites) and the Platte and Elkhorn Rivers (high-impact agricultural sites).
2012-03-01 | E-GEOD-33436 | biostudies-arrayexpress
Project description:We investigated ecotoxicological effects and toxicogenomic responses in fathead minnows (Pimephales promelas) exposed to an environmentally-relevant concentration (0.83 mg/L) of the munitions compound cyclotrimethylenetrinitramine (RDX) in one year and multi-generational assays. In the one year assay, RDX effects were discerned by comparing breeding groups reared in control or RDX-exposure conditions for one year. RDX had no detectable effect on gonad-somatic index, or condition factor in females assayed at 1 day and at 1, 3, 6, 9, and 12 months, however the liver-somatic index was significantly increased versus controls only at the 12 month time point. RDX had no effect on live-prey capture rates at all time points assayed and no significant impacts on egg production, fertilization or hatch success in the 1-year exposure trial. Genomic analyses indicated that RDX exposure caused limited differential expression of transcripts within time points and no functional conservation of effects indicative of RDX exposure among time points for either brain or liver tissues in the one year exposure. In the multi-generational assay, the effects of acute (96h) exposure to RDX were compared in fish reared to the F2 generation in either control or RDX-exposure conditions. The RDX-reared fish were not observed to have appreciably enhanced RDX tolerance versus the control-reared fish. However, significant differences in gene expression were observed among the control and RDX-reared fish related to neuro-excitatory glutamate metabolism, sensory signaling and processes in neurological development. In total, our results indicate that exposure to an RDX concentration approximating maximum levels observed in the field (0.83 mg/L) caused limited impacts in fathead minnows in a one year exposure, however caused altered expression in genes involved in neural function in a multi-generational exposure. Adult fathead minnows were exposed to 0.83 mg/L (0.15 mg/L standard deviation) in experimental units including 2 male and 4 fish. Five replicate males were randomly sampled with replacement from each of 8 control and 8 RDX-exposed experimental units at 1d, 1mo, 3mo, 6mo, 9mo and 12mo sampling periods. Liver tissue was investigated for differential expression in response to RDX exposure.
2010-07-30 | E-GEOD-21100 | biostudies-arrayexpress