Urine samples were derived from a variety of archived industry-led studies, outlined in the dataset. The purpose was to measure a targeted set of miRNA targets that were represented in the Thermo Fisher TLDA A and TLDA B card sets in Figure 2. These case studies were selected due to probable nephrotoxicity, associated with published or internal records. These clinical markers and histopath evidence was included in Table 1 associated dataset. Given specific nephron toxicity, this experiment would determine miRNA candidates that may be specific toxicity biomarkers. This analysis set up the Venn Analysis in Figure 3, which specified candidates for nephron-specific analyses. This dataset is associated with the following publication: Chorley, B., H. Ellinger-Ziegelbauer, M. Tackett, F. Simutis, A. Harrill, J. McDuffie, E. Atabakhsh, R. Nassirpour, L. Whiteley, J. Léonard, G. Carswell, E. Harpur, C. Chen, and J. Gautier. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 180(1): 1-16, (2021).

To determine nephron specificity of microRNA expression that may be associated as toxicity biomarker seen in the urine, laser-capture microdissection (LCM) was performed on the 4 major segment of the nephron in control rat samples. These samples were sent to Bayer for candidate digital drop PCR measurements, NIEHS for smallRNA-seq measurements, and Abcam for FirePlex measurements. smallRNA-seq measurements were used as global assessment of miRNA expression in these segments. FirePlex and ddPCR were used as medium to low number candidate assessments, respectively, of miRNA candidates, based on seq and urine data. "Data associated with Fig 4" summarizes the ddPCR findings. "Data Associated with Figure 5" and "Data Associated with Figure 6" summarize the smallRNA-seq findings. "Data Associated with Figure 7" summarize the FirePlex findings. "Data associated with Figure 8_9" summarize the correlations of these measurements. The cumlmination of these data determine nephron-specific and enriched expression of miRNAs, that are potential candidates of toxicity markers that could leak into the urine upon chemical exposure. This dataset is associated with the following publication: Chorley, B., H. Ellinger-Ziegelbauer, M. Tackett, F. Simutis, A. Harrill, J. McDuffie, E. Atabakhsh, R. Nassirpour, L. Whiteley, J. Léonard, G. Carswell, E. Harpur, C. Chen, and J. Gautier. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 180(1): 1-16, (2021).

To determine nephron specificity of microRNA expression that may be associated as toxicity biomarker seen in the urine, laser-capture microdissection (LCM) was performed on the 4 major segment of the nephron in control rat samples. These samples were sent to Bayer for candidate digital drop PCR measurements, NIEHS for smallRNA-seq measurements, and Abcam for FirePlex measurements. smallRNA-seq measurements were used as global assessment of miRNA expression in these segments. FirePlex and ddPCR were used as medium to low number candidate assessments, respectively, of miRNA candidates, based on seq and urine data. "Data associated with Fig 4" summarizes the ddPCR findings. "Data Associated with Figure 5" and "Data Associated with Figure 6" summarize the smallRNA-seq findings. "Data Associated with Figure 7" summarize the FirePlex findings. "Data associated with Figure 8_9" summarize the correlations of these measurements. The cumlmination of these data determine nephron-specific and enriched expression of miRNAs, that are potential candidates of toxicity markers that could leak into the urine upon chemical exposure. This dataset is associated with the following publication: Chorley, B., H. Ellinger-Ziegelbauer, M. Tackett, F. Simutis, A. Harrill, J. McDuffie, E. Atabakhsh, R. Nassirpour, L. Whiteley, J. Léonard, G. Carswell, E. Harpur, C. Chen, and J. Gautier. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 180(1): 1-16, (2021).

Excel file of miRNA data. This dataset is associated with the following publication: Chen, H., S. Masood, A. Rappold, D. Diaz Sanchez, J. Samet, and H. Tong. The effects of controlled ozone exposure on circulating microRNAs and vascular and coagulation biomarkers: a mediation analysis. Non-Coding RNA. MDPI, Basel, SWITZERLAND, 9(4): 43, (2023).

This dataset is a project file generated by BMDExpress 2.2 SW (Sciome, Research Triangle Park, NC). It contains gene expression data for livers of rats exposed to 4 chemicals (crude MCHM, neat MCHM, DMPT, p-toluidine) and kidneys of rats exposed to PPH. The project file includes normalized expression data (GeneChip Rat 230 2.0 Array) using 7 different pre-processing methods (RMA, GCRMA, MAS5.0, MAS5.0_noA calls, PLIER, PLIER16, and PLIER16_noA calls); differentially expressed probe-sets detected by William's method (p<0.05, and minimum fold change of 1.5); probeset-level and pathway-level BMD and BMDL values from transcriptomic dose-response modeling. This dataset is associated with the following publication: Mezencev, R., and S. Auerbach. The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PLOS ONE. Public Library of Science, San Francisco, CA, USA, 15(5): e0232955, (2020).

PubMed was searched for the terms microRNA and biomarker in addition to blood (blue), urine (orange), saliva (grey), or cerebrospinal fluid (yellow). The graph in the paper displays the number of total annual publications over the past 16 years and the actual numbers used generate this graph are in incuded in the attached spreadsheet. A near annual doubling of publications occurred from the years 2009 until 2015, whereas only a mere 4% increase in annual publications from 2015 until 2018 was noted. While a number of factors can contribute to these publication trends, this indicates an overall cooling of research interest in biofluid-based microRNA biomarker development. This dataset is associated with the following publication: Chorley, B., E. Atabakhsh, G. Doran, J. Gautier, H. Ellinger-Ziegelbauer, D. Jackson, T. Sharapova, P. Yuen, R. Church, P. Couttet, R. Froetschl, J. McDuffie, V. Martine, P. Pande, L. Peel, C. Rafferty, F. Simutis, and A. Harrill. Methodological considerations for measuring biofluid-based microRNA biomarkers. CRITICAL REVIEWS IN TOXICOLOGY. Taylor & Francis Group, London, UK, 51(3): 264-282, (2021).

PubMed was searched for the terms microRNA and biomarker in addition to blood (blue), urine (orange), saliva (grey), or cerebrospinal fluid (yellow). The graph in the paper displays the number of total annual publications over the past 16 years and the actual numbers used generate this graph are in incuded in the attached spreadsheet. A near annual doubling of publications occurred from the years 2009 until 2015, whereas only a mere 4% increase in annual publications from 2015 until 2018 was noted. While a number of factors can contribute to these publication trends, this indicates an overall cooling of research interest in biofluid-based microRNA biomarker development. This dataset is associated with the following publication: Chorley, B., E. Atabakhsh, G. Doran, J. Gautier, H. Ellinger-Ziegelbauer, D. Jackson, T. Sharapova, P. Yuen, R. Church, P. Couttet, R. Froetschl, J. McDuffie, V. Martine, P. Pande, L. Peel, C. Rafferty, F. Simutis, and A. Harrill. Methodological considerations for measuring biofluid-based microRNA biomarkers. CRITICAL REVIEWS IN TOXICOLOGY. Taylor & Francis Group, London, UK, 51(3): 264-282, (2021).

Analytical chemistry and toxicological assessment of microcystin-LR toxin standards from seven vendors; a comparison of mass, purity and toxicity based on label mass. This dataset is associated with the following publication: Lang, J., D. Jenkins-Hill, N. Chernoff, J. Schmid, M. Strynar, J. McCord, C. Rosal, and T.L. Thanh. Variability of Microcystin-LR Standards Available from Seven Commercial Vendors. Toxins. MDPI, Basel, SWITZERLAND, 14(10): 705, (2022).

Analytical chemistry and toxicological assessment of microcystin-LR toxin standards from seven vendors; a comparison of mass, purity and toxicity based on label mass. This dataset is associated with the following publication: Lang, J., D. Jenkins-Hill, N. Chernoff, J. Schmid, M. Strynar, J. McCord, C. Rosal, and T.L. Thanh. Variability of Microcystin-LR Standards Available from Seven Commercial Vendors. Toxins. MDPI, Basel, SWITZERLAND, 14(10): 705, (2022).

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