title: Bulk tumor RNA-seq of homo sapiens: Merkel Cell Carcinoma: Sample 268
design: Briefly, patient tumor biopsies were either fresh-frozen and stored in liquid nitrogen or immediately treated with RNAlater (Thermo Fisher Scientific) and stored at –80°C. Each RNAlater-treated sample was homogenized with the QIAGEN TissueRuptor II, and RNA was isolated with the AllPrepDNA/RNA Mini Kit (QIAGEN). The NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare sequencing libraries. Paired end sequencing (PE150) was performed on the NovaSeq 6000 system (Illumina). Sequences were mapped and quantified to the decoy-aware, concatenated transcriptome of GRCh38.p13 (Ensembl, version 102) and MCPyV (R17b) using Salmon. Gene-level counts were generated via TxImport, and normalized counts were generated via DESeq2. Samples were considered virus positive if the number of normalized MCPyV LT counts was greater than 100 and the number of normalized ST counts was greater than 10.