Spatial transcriptome analysis of muscle sections from Icos-/- NOD mice with established myositis

Icos-/- NOD mice are a model of spontaneous myositis. By using Nanostring GeoMx technology (Mouse WTA), we aimed to investigate the differences in gene expression between myofibers of Icos+/+ NOD (WT) mice and myofibers from Icos-/- NOD mice either in direct contact or not with large infiltrate clusters. Using Nanostring technology, the transcriptomes of myofibers vs. immune cells were analysed separately by using desmin and CD45 markers. The present study includes the following AOIs: 4 AOIs from Icos+/+ NOD muscle (n=4 mice, 1 AOI/mouse, desmin+CD45-) , 6 AOIs from Icos-/- NOD muscle not directly adjacent to immune cell infiltrates (PROX, n=6 mice, 1 AOI/mouse, desmin+CD45-), 8 AOIs from Icos-/- NOD muscle directly adjacent to immune cell infiltrates (ADJ, n=6 mice, 1-2 AOI/mouse, desmin+CD45-), 8 AOIs from Icos-/- NOD muscle coresponsing to immune cell infiltrates (INF, n=6 mice, 1-2 AOI/mouse, desmin-CD45+).