Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using two-colour Agilent microarrays

Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen (GSE48644) and formalin-fixed paraffin embedded (FFPE; this study) samples using two-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 one-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles. In this experiment we examined the transcriptional response of 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. Samples were formalin-fixed (for 18hrs or 3wks) and paraffin embedded. There were a total of 8 samples included in the final analysis of the two-colour microarrays. We used a reference design (using pooled sample cDNA as a reference), randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).