mSCC genome

The murine KLN205 cell line (Cellosaurus ID: CVCL_3533; derived from DBA/2 strain) was obtained from the American Type Culture Collection (ATCC; catalog no. CRL-1453), while the mEC25 cell line (Cellosaurus ID: CVCL_C6JH; derived from C57BL/6 strain) was generously provided as a gift from a collaborating laboratory. Both cell lines were expanded using standard cell culture protocols, including maintenance in appropriate growth media supplemented with fetal bovine serum and antibiotics to prevent contamination. To confirm tumorigenicity, cells were subcutaneously injected into immunocompetent female C57BL/6 or DBA/2 mice, respectively, and monitored for tumor formation over a period of 4-6 weeks, with histological verification of neoplastic growth via hematoxylin and eosin staining where necessary.Independent clonal cultures were established for both the mEC25 and KLN205 cell lines, with stable passaging maintained for over 3 months to ensure genetic homogeneity and minimize drift. Whole-genome sequencing (WGS) was performed on two independent clones of KLN205. For mEC25, WGS was conducted on three independent clones, supplemented by whole-exome sequencing (WES) on two of these clones (n=2). Peripheral blood samples from female C57BL/6 and DBA/2 mice served as matched germline controls to facilitate variant calling and somatic mutation analysis, enabling the identification of tumor-specific genomic alterations while accounting for strain-specific polymorphisms.