1. Female B6C3F1 mice (n=4) Furan (0 or 8 mkd) 3 weeks RNA Extraction Agilent 8x60K microarrays: 1- and 2-color arrays Illumina HighSeq RNA-seq: PolyA and ribodepletion Global gene expression analysis 18hrs 3wks in formalin Paraffin Embedding Frozen - 80°C Divide into three sections Suppl. Fig. S1. Experimental Design. Mice were exposed orally to furan for 21 days (N = 4 per group). Liver was sectioned into three, with one section preserved by flash freezing, the second preserved in formalin for 18 hours followed by paraffin embedding, the third preserved in formalin for 3 weeks prior to paraffin embedding. RNA was extracted from each of these liver samples and every sample was subject to analysis by: (1) one- color DNA microarrays; (2) two-color DNA microarrays; (3) poly-A RNA-sequencing; or (4) ribo-depletion RNA-sequencing.

2. Suppl. Fig. S2. Pathway analysis for (A) ribo-depletion and (B) polyA- enrichment, and (C) 1-colour microarrays, (D) 2-colour microarrays, showing the top 15 enriched pathways for the fresh-frozen samples and enrichment levels of these pathways in the corresponding FFPE samples (pathway significance was calculated in IPA using a Fisher Exact test, -log(p value)=1.3 corresponds to a p=0.05). Venn diagrams show the overlap of the top 15 pathways in each fresh-frozen, 18hr FFPE, and 3wk FFPE. For all analyses, all (i.e.: unmapped) differentially expressed genes with FDR p +/-1.5 were used. A B

3. C D

4. Supplemental Table S1. RNA quality.