Figure 2
From: Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles
Heat map of median centered log2(RSEM +1) of nearly 1800 genes from FFPE specimens subjected to a 1, 2, 3, or 12 h delay-to-fixation (n = 30 for each timepoint) and case-matched snap-frozen controls (n-30). FFPE specimens displayed higher gene expression than case-matched snap-frozen controls for the majority of FFPE samples examined, regardless of delay-to-fixation. The color bar indicates the tissue/tumor of origin (red-Kidney/renal carcinoma, green-Ovarian/fallopian tube and peritoneal carcinoma, purple-Colon/colon adenocarcinoma). Interestingly, 24 FFPE samples show profiles similar to their snap-frozen control counterparts (indicated by the colored up arrows). Differences between the profiles of these 24 FFPE samples and the remaining FFPE samples were not associated with contributing medical institution, time-to-fixation, density of tumor cells, or even case. Specimens displaying DNA contamination (4-4, 59-4, 59-3, and 59-2) grouped together. Specimens 4-4 (highest level of DNA contamination) and 51-4 (lowest amount of usable material) are indicated by black arrows. The scale indicates log2 log2(RSEM +1) values.
