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 sets included in this study: Differential Expressed gene lists for nano Cu CuCl2 treated HepG2 cells through RNA sequencing. Differential Expressed microRNA lists for nano Cu and CuCl2 treated HepG2 cells through small RNA sequencing. Sequencing data was quantified using Partek annotation and the STAR-2.5.3a aligner, aligned to human genome hg19. Normalization and contrast were performed using DESeq2. MicroRNA expression was quantified with mirDeep2. Benjamini-Hochberg method for multi-testing correcton was included in DESeq2.

Background High density cDNA microarray technology provides a powerful tool to survey the activity of thousands of genes in normal and diseased cells, which helps us both to understand the molecular basis of the disease and to identify potential targets for therapeutic intervention. The promise of this technology has been hampered by the large amount of biological material required for the experiments (more than 50 μg of total RNA per array). We have modified an amplification procedure that requires only 1 μg of total RNA. Analyses of the results showed that most genes that were detected as expressed or differentially expressed using the regular protocol were also detected using the amplification protocol. In addition, many genes that were undetected or weakly detected using the regular protocol were clearly detected using the amplification protocol. We have carried out a series of confirmation studies by northern blotting, western blotting, and immunohistochemistry assays. Results Our results showed that most of the new information revealed by the amplification protocol represents real gene activity in the cells. Conclusion We have confirmed a powerful and consistent cDNA microarray procedure that can be used to study minute amounts of biological tissue.

Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed. More accurate measures are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. A general procedure for analyzing cDNA microarray data is proposed and validated. It is shown that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines.

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).

Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real time PCR (qRT PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two step principles used for miRNA qRT PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values.

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).

These data are associated with the figures and tables presented in the manuscript "Early microRNA responses in rodent liver mediated by furan exposure establish dose thresholds for later adverse outcomes". Each spreadsheet contains the data for each Figure and metadata describes each column and/or row of data. For access to the smallRNA-seq files, please follow link provided and supply the reviewer key code "mjsnewymzlollmz".