canonical pathways for each concentration of nano Cu and CuCl2 after upload the DEG lists of each concentration to Ingenuity Pathway Analysis

canonical pathways for each concentration of nano Cu and CuCl2 after upload the DEG lists of each concentration to Ingenuity Pathway Analysis

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).

Differential expressed gene lists and altered canonical pathways in HepG2 cells after CeO2 particle treatment. This dataset is associated with the following publication: Thai, S., C. Jones, B. Robinette, H. Ren, B. Vallanat, A. Astriab Fisher, and K. Kitchin. Differential genomic effects of four nano-sized and one micro-sized CeO2 particles on HepG2 cells. Materials Express. American Scientific Publishers, VALENCIA, CA, USA, 13(10): 1799-1811, (2023).

Differential expressed gene lists and altered canonical pathways in HepG2 cells after CeO2 particle treatment. This dataset is associated with the following publication: Thai, S., C. Jones, B. Robinette, H. Ren, B. Vallanat, A. Astriab Fisher, and K. Kitchin. Differential genomic effects of four nano-sized and one micro-sized CeO2 particles on HepG2 cells. Materials Express. American Scientific Publishers, VALENCIA, CA, USA, 13(10): 1799-1811, (2023).

RNA-seq data from HepaRG cells exposed for 2 hours to microcystin-LR and -RR at multiple concentrations each. This dataset is associated with the following publication: Biales, A., D. Bencic, R. Flick, A. Delacruz, D. Gordon, and W. Huang. Global transcriptomic profiling of microcystin-LR or -RR treated hepatocytes (HepaRG).. Toxicon: X. Elsevier B.V., Amsterdam, NETHERLANDS, 8: 100060, (2020).

data was from HepG2 cells treated with nano-silver particles using silver nitrate as negative controls. Differentially expressed messenger RNA and microRNA were obtained by RNA sequencing and data analysis. Differentially expressed RNA and microRNA lists were than uploaded to Ingenuity Pathway Analysis to find the pathways altered by the differentially expressed genes. This dataset is associated with the following publication: Thai, S., C. Jones, B. Robinette, H. Ren, B. Vallanat, A. Fisher, and K. Kitchin. Effects of Silver Nanoparticles and Silver Nitrate on mRNA and microRNA Expression in Human Hepatocellular Carcinoma Cells (HepG2). Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 21(11): 5414-5428, (2021).

data was from HepG2 cells treated with nano-silver particles using silver nitrate as negative controls. Differentially expressed messenger RNA and microRNA were obtained by RNA sequencing and data analysis. Differentially expressed RNA and microRNA lists were than uploaded to Ingenuity Pathway Analysis to find the pathways altered by the differentially expressed genes. This dataset is associated with the following publication: Thai, S., C. Jones, B. Robinette, H. Ren, B. Vallanat, A. Fisher, and K. Kitchin. Effects of Silver Nanoparticles and Silver Nitrate on mRNA and microRNA Expression in Human Hepatocellular Carcinoma Cells (HepG2). Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 21(11): 5414-5428, (2021).

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).

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).