Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using one-colour Agilent microarrays. Mus musculus

Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles. Overall design: In this study we examined the transcriptional response in liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure. Each dose group had 4 biological replicates. There were a total of 8 samples included in the final analysis of the one-colour microarrays. We used a randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).