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. Overall design: 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+).