Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), 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. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (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 experiment we examined the transcriptional response of liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 1, 2, 4, or 8 mg/kg bodyweight per day furan (or vehicle control) and sacrificed four hours after the final exposure. Each dose group had 5 biological replicates. Samples were formalin-fixed (for 18 hours or 3 weeks) and paraffin embedded. We used a randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).