Transcriptomic Profiling of FFPE Samples

RNA was extracted from FFPE slides of 21 patients using the ReliaPrep™ FFPE Total RNA Miniprep kit (Promega, Madison, WI, USA). Extracted RNA was then synthesized into cDNA using the TruSeq RNA Exome Kit (Illumina, San Diego, CA, USA), and an RNA sequencing dataset was generated using the Nova 6000 platform (Illumina). The raw data were quantified using the STAR [19 (link)] and RSEM [20 (link)] quantification tools, and differentially expressed gene (DEG) analysis was performed using DESeq2 [21 (link)]. The threshold for identifying DEGs was adjusted to absolute log2 fold change ≥ 1 and p < 0.05. The DEGs were plotted in a volcano plot graph using the “ggplot” package in R.