Fig. 3

Spatial transcriptomics in MOG-EAE. A Experimental workflow of barcode-based spatial transcriptomics. Images were created with BioRender. B Cartoon depicting the anatomical location of barcoded spots in the clustering and in C. Clustering shows the spots color-coded according to the Seurat clustering (graph-based clustering and hierarchical cluster merging). Images were created with Loupe Browser. Scale bar: 1 mm. C UMAP visualization of all spots, split by condition: healthy (n = 2), early EAE and late EAE (n = 3, per condition). Seurat clusters are color-coded, labeled and annotated (in groups) by their anatomical location. Image created with Loupe Browser. D Subsets show the color-coding according to the two subsets for DGE-testing: “NAWM” (purple) and “WML” (yellow) and the excluded non-white-matter spots (teal). UMAP visualization of all spots split by condition: early EAE and late EAE (n = 3, per condition). Seurat clusters are color-coded: NAWM” (purple) and “WML” (yellow)