RNA and whole exome sequencing of a solar-simulated light-induced murine cutaneous squamous cell carcinoma model

To enable investigations of the neoantigen profile and T cell response to cutaneous squamous cell carcinoma (cSCC), we created a panel of transplantable, solar-simulated UV light-induced, cSCC cell lines in BALB/C mice. Cell lines from three cSCC tumors from BALB/C mice underwent whole exome sequencing. Subsequently, six clonal cSCC cell lines were generated from the three tumor cell lines and underwent whole exome and RNA sequencing with six biological replicates of RNA sequencing. One of the six clonal cell lines underwent in vivo passage in a wild-type mouse followed by readaptation to culture. This progeny cell line also underwent whole exome and RNA sequencing, with two replicates of RNA sequencing. Normal skin from a BALB/C mouse also underwent whole exome sequencing as a germline comparison. DNA and RNA were extracted from the cSCC cell lines using the DNeasy Blood and Tissue Kit (QIAGEN Cat. No. 69504) and RNeasy Mini kit (QIAGEN Cat. No. 74104), respectively. The manufacturer's instructions were used to extract DNA and RNA using RNase A (QIAGEN Cat. No. 19101) and DNase I (QIAGEN Cat. No. 79254) treatments, respectively. Whole exome sequencing (WES) at 80x coverage and RNA sequencing (RNAseq) with 20 million read pairs were performed at the Yale Center for Genome Analysis. Libraries were prepared using the Roche Diagnostics KAPA Hyper kit following the manufacturer's instructions. Exome enrichment was done using the Agilent SureSelect XT Mouse All Exon kit following the manufacturer's instructions. Libraries concentration and quality control were performed using qPCR (Roche Diagnostics) and Tapestation (Agilent). The samples were sequenced in a 2 x 100 bp paired-end setting on an Illumina NovaSeq 6000 system according to the manufacturer's protocol.