This dataset presents the full hepatic transcriptomes of fathead minnows (Pimephales promelas) caged for four days at multiple sites within the Milwaukee Estuary area of concern and additional control sites. At these same sites over the same period of exposure, time integrated water samples were collected and assessed for the presence of over 170 relevant chemical analytes. Access to both full sequencing of fish samples as well as water contaminant data will allow others to explore the health of these ecosystems. This dataset is associated with the following publication: Garcia-Reyero, N., M. Arick II, A. Woolard, M. Wilbanks, J. Mylroie, K. Jensen, M. Kahl, D. Feifarek, S. Poole, E. Randolph, J. Cavallin, B. Blackwell, D. Villeneuve, G. Ankley, and E. Perkins. Male fathead minnow transcriptomes and associated chemical analytes in the Milwaukee estuary system. Scientific Data. Springer Nature, New York, NY, USA, 9: 476, (2022).

The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. This dataset is associated with the following publication: Villeneuve, D., M. Le, M. Hazemi, A. Biales, D. Bencic, K. Bush, R. Flick, J. Martinson, M. Morshead, K. Santana Rodriguez, K. Vitense, and K. Flynn. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 4: 100099, (2022).

The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. This dataset is associated with the following publication: Villeneuve, D., M. Le, M. Hazemi, A. Biales, D. Bencic, K. Bush, R. Flick, J. Martinson, M. Morshead, K. Santana Rodriguez, K. Vitense, and K. Flynn. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 4: 100099, (2022).

The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks. This dataset is associated with the following publication: Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).

The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks. This dataset is associated with the following publication: Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line. This dataset is associated with the following publication: Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line. This dataset is associated with the following publication: Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

Data for "Flynn, K., Le, M., Hazemi, M. et al. Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action. Arch Environ Contam Toxicol 86, 346–362 (2024). https://doi.org/10.1007/s00244-024-01064-y". Portions of this dataset are inaccessible because: N/A. They can be accessed through the following means: All sequence data reported in this manuscript are accessible via the Gene Expression Omnibus (BioProject PRJNA104613). Format: N/A. This dataset is associated with the following publication: Flynn, K., M. Le, M. Hazemi, A. Biales, D. Bencic, B. Blackwell, K. Bush, R. Flick, J. Hoang, J. Martinson, M. Morshead, K. Santana Rodriguez, E. Stacy, and D. Villeneuve. Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY. Springer, New York, NY, USA, 86(4): 346-362, (2024).

This data set describes experiments that were conducted to investigate whether exposure of male fathead minnows to environmentally-relevant estrone concentrations would result in elevated plasma 17β-estradiol concentrations in the fish. Secondly, we sought to establish whether observed elevations in plasma 17β-estradiol occurred as a result of the conversion of external estrone by the fish using an approach involving exposure of the fish to 13C-labeled estrone. Endpoints reported in the dataset include plasma 17β-estradiol and estrone concentrations, plasma vitellogenin concentrations, hepatic vitellogenin mRNA, 13C-labeled plasma 17β-estradiol and estrone concentrations, and testicular and/or hepatic expression of aromatase and several hydroxysteroid dehydrogenases involved in estrone metabolism. This dataset is associated with the following publication: Ankley, G., D. Feifarek, B. Blackwell, J. Cavallin, K. Jensen, M. Kahl, S. Poole, E. Randolph, T. Saari, and D. Villeneuve. Reevaluating the significance of estrone as an environmental estrogen (article). ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51: 4705-4713, (2017).

This data set describes experiments that were conducted to investigate whether exposure of male fathead minnows to environmentally-relevant estrone concentrations would result in elevated plasma 17β-estradiol concentrations in the fish. Secondly, we sought to establish whether observed elevations in plasma 17β-estradiol occurred as a result of the conversion of external estrone by the fish using an approach involving exposure of the fish to 13C-labeled estrone. Endpoints reported in the dataset include plasma 17β-estradiol and estrone concentrations, plasma vitellogenin concentrations, hepatic vitellogenin mRNA, 13C-labeled plasma 17β-estradiol and estrone concentrations, and testicular and/or hepatic expression of aromatase and several hydroxysteroid dehydrogenases involved in estrone metabolism. This dataset is associated with the following publication: Ankley, G., D. Feifarek, B. Blackwell, J. Cavallin, K. Jensen, M. Kahl, S. Poole, E. Randolph, T. Saari, and D. Villeneuve. Reevaluating the significance of estrone as an environmental estrogen (article). ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51: 4705-4713, (2017).