Gene expression analysis of livers from female B6C3F1 mice exposed to carcinogenic and non-carcinogenic doses of furan, with or without bromodeoxyuridine (BrdU) treatment.
Standard methodology for identifying chemical carcinogens is both time-consuming and resource intensive. Researchers are actively investigating how new technologies can be used to identify chemical carcinogens in a more rapid and cost-effective manner. Here we performed a toxicogenomic case study of the liver carcinogen furan. Full study and mode of action details were previously published in the Journal of Toxicology and Applied Pharmacology. Female B6C3F1 mice were sub-chronically treated with two non-carcinogenic (1 and 2 mg/kg bw) and two carcinogenic (4 and 8 mg/kg bw) doses of furan for 21 days. Half of the mice in each dose group were also treated with 0.02% bromodeoxyuridine (BrdU) for five days prior to sacrifice [13]. Agilent gene expression microarrays were used to measure changes in liver gene and long non-coding RNA expression (published in Toxicological Sciences). Here we describe the experimental and quality control details for the microarray data. We also provide the R code used to analyze the raw data files, produce fold change and false discovery rate (FDR) adjusted p values for each gene, and construct hierarchical clustering between datasets.
Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada ; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa K1S 5B6, Canada.
Anna Francina
AF
Webster
Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada.
Andrew
A
Williams
ILS, P.O. Box 13501, Research Triangle Park, NC 27709, USA.
Leslie
L
Recio
Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada.
Carole L
CL
Yauk
Dose–response; Furan; Liver cancer; Microarray; Statistical analysis in R