Figure 3
From: Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples
Effects of formalin fixation on detection of chemical treatment responses. (a) Venn diagram showing overlap in significant phenobarbital (PB)-induced differentially expressed genes (DEGs, FDR-adjusted p-value < 0.05, ± twofold-change) across preservation groups: frozen control (FR), 70% ethanol-fixed (FR > OH), frozen first then 18-h formalin-fixed (FR > FFPE), and 18-h formalin-fixed (FFPE) liver tissue samples. FR > OH, FR > FFPE, and FFPE samples were all paraffin-embedded. (b) Expression pattern of top 10 PB-induced differentially expressed genes. Across preservations, FR > OH, FR > FFPE, and FFPE resulted in significant reductions of counts per million (CPM) gene counts for all preservations relative to frozen control (FR). Error bars represent standard error. Significant differences between preservation group compared to frozen were determined by two-tailed Wilcoxon signed-rank test with Holm correction. **p-value = 0.0029, *p-value = 0.01 (c) Significant upstream regulators (Right-Tailed Fisher’s Exact Test, p-value < 0.05) predicted from PB-induced DEG patterns across preservation groups. « indicates CAR, PXR, and PB. (d) Z-scores of upstream regulators matched to significant p-values with positive z-scores predicting activation and negative scores predicting repression of regulator. « indicates CAR, PXR, and PB.
