Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells. This dataset is associated with the following publication: Thai , S., K. Wallace , C. Jones , H. Ren , B. Castellon, J. Crooks , E.A. Grulke, and K. Kitchin. Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells. Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 15(12): 9925-37, (2015).

transformed raw data. This dataset is associated with the following publication: Kitchin, K., J. Richards, B. Robinette, K. Wallace, N. Coates, B. Castellon, and E. Grulke. Biochemical effects of some CeO2, SiO2, and TiO2 nanomaterials in HepG2 cells. CELL BIOLOGY AND TOXICOLOGY. Springer, New York, NY, USA, 2(35): 129-145, (2019).

transformed raw data. This dataset is associated with the following publication: Kitchin, K., J. Richards, B. Robinette, K. Wallace, N. Coates, B. Castellon, E. Grulke, and J. Kou. Biochemical effects of some CeO2, SiO2, and TiO2 nanomaterials in HepG2 cells.. CELL BIOLOGY AND TOXICOLOGY. Springer, New York, NY, USA, 35(2): 129-145, (2019).

The data set is a matrix of cellular biochemical (metabolites) in HepG2 cells treated with various metal oxide nanomaterials composed of CeO2, SiO2 and CuO. This dataset is associated with the following publication: Kitchin, K., S. Stirdivant, B. Robinette, B. Castellon, and X. Liang. Metabolomic effects of CeO2, SiO2 and CuO metal oxide nanomaterials on HepG2 cells. Particle and Fibre Toxicology. BioMed Central Ltd, London, UK, 14(50): 1-16, (2017).

transformed raw data of biochemical paramiters. This dataset is associated with the following publication: Kitchin, K., J. Richards, B. Robinette, K. Wallace, N.H. Coates, B. Castellon, E. Grulke, J. Kou, and R. Varma. Biochemical Effects of Silver Nanomaterials in Human Hepatocellular Carcinoma (HepG2) Cells. Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 20(9): 5833-5858, (2020).

Signaling pathways from IPA: canonical pathways obtained by uploading differentially expressed genes onto IPA to get the corresponding pathways altered by the chemicals. Figure 4 ABCDHILM ROS final: Excel file with raw data and calculated fold change for the ROS (Deep Red) assay on 8 nanoparticles. Data files for tables: this file include physical-chemical properties of the 8 NPs (worksheet 1), sizing and zeta potential from zeta sizer (worksheet 2&3) and numbers of differentially expressed genes (DEGs) (worksheet 4). Data files for figure 5 to 11: physical -chemical properties of the NPs, raw data and calculation for ROS-RNS, 8-oxo-dG, AP sites, endogenous DNA adducts, 4-HNE, and MDA adducts. This dataset is associated with the following publication: Thai, S., C. Jones, G. Nelson, B. Vallanat, M. Killius, J. Crooks, w. Ward, C. Blackman, and J. Ross. Differential effects of Nano TiO2 and CeO2 on normal human lung epithelial cells in vitro. Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 19(11): 6907-6923, (2019).

We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants. FASTQ files and read counts data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) (GSE152128). This dataset is associated with the following publication: Lee, F., I. Shah, Y.T. Soong, J. Xing, I.C. Ng, F. Tasnim, and H. Yu. Reproducibility and Robustness of High-Throughput S1500+ Transcriptomics on Primary Rat Hepatocytes for Chemical-Induced Hepatotoxicity Assessment. Current Research in Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 2: 282-295, (2021).

Datasets used in RD-023418: Adverse Outcome Pathway-Driven Identification of Rat Hepatocarcinogens in Short-Term Assays. This dataset is associated with the following publication: Rooney, J., T. Hill, C. Qin, F. Sistare, and C. Corton. Adverse outcome pathway-driven identification of rat liver tumorigens in short-term assays. TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 356: 99-113, (2018).

the zip files contain outputs from the R-analysis for the nanosilver experiments. This dataset is associated with the following publication: Strickland, J., W. LeFew, J. Crooks, D. Hall, J. Ortenzio , K. Dreher , and T. Shafer. In vitro screening of silver nanoparticles and ionic silver using neural networks yields differential effects on spontaneous activity and pharmacological responses.. TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 355(11): 1-8, (2016).

hyperspectral imaging data, images , flow cytometry histograms. This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: contact robert zucker by e-mail zucker.robert@epa.gov. Format: the imaging is in JP2 and ND 2 nikon files . the flow cytometry is in FSC3.0 format which is not uploadable. This dataset is associated with the following publication: Zucker, R., J. Ortenzio, L. Degn, J. Lerner , and W. Boyes. Biophysical Comparison of Four Silver Nanoparticles Coatings using Microscopy, Hyperspectral Imaging and Flow Cytometry.. PLoS ONE. Public Library of Science, San Francisco, CA, USA, 1-24, (2019).