Abstract:
This is a laboratory study of oil chemicals that induce changes in gene expression in the Hepa1c1c2 cell line. Dose response profiles, as assessed by gene expression, were determined for selected polycyclic aromatic hydrocarbons (PAHs) found in oil. These gene expression dose responses were compared across several marker genes (CYP1A1, 1B1, 1A2, NQO1, etc.,) to determine relationships to cytotoxicity of PAHs.
Suggested Citation:
Wickliffe, Lichtler. 2020. Metabolic gene transcriptional responses in Hepa1c1c7 cells. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N37BNKGD
Data Parameters and Units:
The dataset includes all of the raw and processed data files used to estimate differences in gene expression among select PAH-responsive genes following defined treatments. Many of the raw files are instrument files used and generated by the hardware in the laboratory in these experiments.
The “PAHs Gene Expression” folder contains several PLTC files, and several folders of gene expressions of several marker genes such as CYP1A1, CYP1A2, CYP1B1, Nqo1, Gclc, and Hmox1. Each folder of the marker gene contains several sets of combinations of an Excel file and a PCRD file for specific exposure of an organic molecule such as chrysene and benzo(a)pyrene. The headers for the Excel file of these marker genes are Well, Fluor (fluorescent dye), Target, Content, Sample, Cq (quantification cycle), Cq Mean, and Cq Std. Dev.
The “PAHs Gene Expression” folder also contains the additional folder titled “Processed Data Files”. This folder includes the processing of data. The headers for the Excel file of these marker genes are Well, Fluor (fluorescent dye), Target, Content, Sample, Cq (quantification cycle), Cq Mean, and Cq Std. Dev.
The “RNA Isolations” folder contains TWBK files and XML files. TWBK files contain data recorded by the nano spectrophotometer, while XML files contain data on concentrations of nucleic acid (RNA) measured and quality of nucleic acid (A260/A280).
The headers for these XML files are Sample ID, User name, Date and Time, Nucleic Acid Conc., Unit (µg/µl), A260 (Absorbance at 260 nm), A280 (Absorbance at 280 nm), 260/280, 260/230, Sample Type (DNA or RNA), and Factor.
PLTD files define the sample details and location in the 96-well microplate format for the real-time thermal cycler used for gene expression studies. Each setup file was created for a separate gene involved in PAH metabolism or response. These were created and used to make experimental setup and design simpler and consistent across the range of PAHs that were tested. They are specific for the Bio-Rad platform that was used (C1000 with CFX96 fluorescence reader) and must be read with Bio-Rad’s software.
Please note that gaps in Excel file denote that there is no data. Transcriptional responses across a range of chemical treatments are measured in arbitrary fluorescence units. These are then normalized to an untreated (vehicle) control to facilitate comparison in the fully processed data.
Methods:
All treatments were carried using defined, equimolar concentrations of selected PAHs including parent compound (unsubstituted) and methylated isomers including some select monomethyl and dimethyl isomers of chrysene.
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