PM Exome-seq
Bulk RNA sequencing was performed on 89 of 93 samples with either confirmed pleural mesothelioma (PM) diagnosis or normal pleura obtained from non-PM malignancy resections. Of these, 71 samples were adjacent to those used for scRNA-seq, while the remaining samples were obtained from the same anatomical site or case. Extracted RNA was shipped on dry ice for library preparation. Polyadenylated RNA was enriched using poly-T oligo–attached magnetic beads, and stranded cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Libraries were sequenced on an Illumina NovaSeq 6000 to a depth of approximately 100 million paired-end 100 bp reads per sample.  Sequencing reads were assessed for mapping rates and library size prior to downstream analysis. Quality-controlled reads were aligned to the human reference genome (hg38) using STAR, and gene-level counts were generated using GENCODE v28 annotation. Raw counts were normalized to transcripts per million (TPM), with library size adjustment performed using trimmed mean of M-values normalization in edgeR.