Mouse Skin Xenium In Situ Spatial Gene Expression

To investigate the effecs of commensal papillomavirus immunity on the homeostasis of highly mutated normal skin, spatial transcriptomics (Xenium, 10x Genomics, Pleasanton, CA) was performed on SKH-1 mouse back skin. The mice were treated with mouse papillomavirus (MmuPV1) or virus-like particles (VLP), followed by UV exposure for 25 weeks. Formalin-fixed, paraffin-embedded (FFPE) mouse back skin samples, infected with MmuPV1 (n = 2, pooled onto one slide) or treated with virus-like particles (VLP; n = 2, pooled onto one slide) followed by UV exposure, were sectioned into 5 µm slices onto Xenium slides. Custom probe hybridization, ligation, amplification, cell segmentation staining, and autofluorescence quenching were then performed using the Xenium In Situ Analyzer.