This data set is composed of Tables, Figures, zip file containing the whole manuscript individual datasets. This dataset is associated with the following publication: Wehmas, L., C. Wood, B. Chorley, C. Yauk, G. Nelson, and S. Hester. Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 170(2): 357-373, (2019).

Dataset includes summary statistics (mean, standard error, sample size) for all endpoints measured and reported in the experiments described in the published manuscript. This dataset is associated with the following publication: Conley, J., C. Lambright, N. Evans, A. Farraj, J. Smoot, R. Grindstaff, D. Jenkins-Hill, J. McCord, E. Medlock Kakaley, A. Dixon, E. Hines, and L. Gray. Dose additive maternal and offspring effects of oral maternal exposure to a mixture of three PFAS (HFPO-DA, NBP2, PFOS) during pregnancy in the Sprague-Dawley rat. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 892: 164609, (2023).

Data processing was conducted using the Anaconda distribution of Python 3.9 and associated libraries. Jupyter notebooks are available at https://github.com/patlewig/nts_pfas. Datasets supporting the manuscript are accessible at https://doi.org/10.23645/epacomptox.26524327. This dataset is associated with the following publication: Patlewicz, G., R. Judson, A. Williams, T. Butler, S. Barone, K. Carstens, J. Cowden, J. Dawson, S. Degitz, K. Fay, A. Lowit, S. Padilla, K. Friedman, M. Phillips, D. Turk, J. Wambaugh, B. Wetmore, and R. Thomas. Development of chemical categories for per- and polyfluoroalkyl substances (PFAS) and the proof-of-concept approach to the identification of potential candidates for tiered toxicological testing and human health assessment. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 31: 100327, (2024).

Dataset includes reduced nitrogen (NHx) concentrations that were collected at Duke Forest, NC and Gainesville, FL using a CSN MetOne SuperSASS and IMPROVE PM sampler from May - October 2017. Using an acid impregnated filter in the CSN and IMPROVE samplers, NHx concentrations were compared to URG annular denuder measurements. Results are summarized in a report: Improving characterization of reduced nitrogen at IMPROVE and CSN monitoring sites (https://www.epa.gov/system/files/documents/2021-11/nhx_summary-report_final.pdf). Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

We screened 44 chemicals in MCF7 cells in concentration response and generated HTTr data using the TempO-Seq hWTv1 assay. First, we provide an outline of the quality of the HTTr data based on a set of QC metrics we developed for this platform. Second, we evaluate the reproducibility and mechanistic accuracy of the HTTr platform using inter-plate analysis of reference samples and comparison of reference chemical treatment effects with CMAP signatures, respectively. Third, we summarize the concentration-dependent HTTr responses for all 44 chemicals to stratify them in terms of their overall effect on the transcriptome. Fourth, we present a new gene signature based concentration-response analysis that provides potency estimates for perturbation of cellular biology (ie, BPACs). This dataset is associated with the following publication: Harrill, J., L. Everett, D. Haggard, T. Sheffield, J. Bundy, C. Willis, R. Thomas, I. Shah, and R. Judson. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 181(1): 68-89, (2021).

We screened 44 chemicals in MCF7 cells in concentration response and generated HTTr data using the TempO-Seq hWTv1 assay. First, we provide an outline of the quality of the HTTr data based on a set of QC metrics we developed for this platform. Second, we evaluate the reproducibility and mechanistic accuracy of the HTTr platform using inter-plate analysis of reference samples and comparison of reference chemical treatment effects with CMAP signatures, respectively. Third, we summarize the concentration-dependent HTTr responses for all 44 chemicals to stratify them in terms of their overall effect on the transcriptome. Fourth, we present a new gene signature based concentration-response analysis that provides potency estimates for perturbation of cellular biology (ie, BPACs). This dataset is associated with the following publication: Harrill, J., L. Everett, D. Haggard, T. Sheffield, J. Bundy, C. Willis, R. Thomas, I. Shah, and R. Judson. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 181(1): 68-89, (2021).

The supplemental information for this paper includes chemical-specific analytical methods, raw instrument data for chemical concentration analysis, processed data for experiments on intrinsic hepatic clearance (CLint -- metabolism) and chemical fraction unbound in the presence of human plasma protein (fup). Figures showing the curve fits for determining CLint are provided. Finally, all data were released publicly as HTTK R Package v1.10.1. This dataset is associated with the following publication: Wambaugh, J., B. Wetmore, C. Ring, C. Nicolas, R. Pearce, G. Honda, R. Dinallo, D. Angus, J. Gilbert, T. Sierra, A. Badrinarayanan, B. Snodgrass, A. Brockman, C. Strock, R. Setzer, and R. Thomas. Assessing Toxicokinetic Uncertainty and Variability in Risk Prioritization. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 172(2): 235-251, (2019).

The supplemental information for this paper includes chemical-specific analytical methods, raw instrument data for chemical concentration analysis, processed data for experiments on intrinsic hepatic clearance (CLint -- metabolism) and chemical fraction unbound in the presence of human plasma protein (fup). Figures showing the curve fits for determining CLint are provided. Finally, all data were released publicly as HTTK R Package v1.10.1. This dataset is associated with the following publication: Wambaugh, J., B. Wetmore, C. Ring, C. Nicolas, R. Pearce, G. Honda, R. Dinallo, D. Angus, J. Gilbert, T. Sierra, A. Badrinarayanan, B. Snodgrass, A. Brockman, C. Strock, R. Setzer, and R. Thomas. Assessing Toxicokinetic Uncertainty and Variability in Risk Prioritization. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 172(2): 235-251, (2019).

This research effort describes a systematic evidence map of relevant health literature for ~150 Per and Polyfluoroalkyl Substances (PFAS). The literature search results, screening and tagging results, and data extractions are all available via download from the provided URLS from HERO, HAWC, and Tableau respectively. In addition, supplemental data files that capture the literature search synonyms, strings, and results are available in the excel file. The word file includes additional information about the results from searching gray literature and other resources consulted, as well as appendixes of human and animal design considerations. The full manuscript contains additional URLs and data with interactive visualizations. This dataset is associated with the following publication: Carlson, L., M. Angrish, A. Shirke, E. Radke-Farabaugh, B. Schulz, A. Kraft, R. Judson, G. Patlewicz, R. Blain, C. Lin, N. Vetter, C. Lemeris, P. Hartman, H. Hubbard, X. Arzuaga, A. Davis, L. Dishaw, I. Druwe, H. Hollinger, R. Jones, J. Kaiser, L. Lizarraga, P. Noyes, M. Taylor, A. Shapiro, A. Williams, and K. Thayer. Systematic Evidence Map for Over One Hundred and Fifty Per- and Polyfluoroalkyl Substances (PFAS). ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 130(5): 1-20, (2022).

The MS Excel file (Dawson et al S2 Supporting information.xlsx) contains multiple sheets containing the training sets, test sets, and predictions for intrinsic metabolic clearance (Clint), fraction unbound in plasma (fup), and bioactivity-exposure ratios (BER), for ToxCast and pharmaceutical-like chemicals. The Word file (Dawson et al S1 Supporting Information.docx) provides additional supporting information on assembly of the training and test sets for Clint, fup, and BER. The data dictionary describes the terms used in the supporting information, S1 and S2. This dataset is associated with the following publication: Dawson, D., B. Ingle, K. Phillips, J. Nichols, J. Wambaugh, and R. Tornero-Velez. Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 55(9): 6505-6517, (2021).