Extended Data Fig. 3: Neuroinflammation specifically alters T helper cell subsets in the dura.
a, Dot plot of selected marker genes to identify different T helper cell subsets in the Dura of naive vs. EAE mice, corresponding to Fig. 1h. Dot size encodes percentage of cells expressing the gene, color encodes the average per cell gene expression level. b, Representative flow cytometry gating strategy to identify Th1, Th17 and Treg cells isolated from Dura of naive (top row) and EAE mice at peak of disease (bottom row). c, Quantification of the percentage of cells in the respective gates as shown in B. Data represented as mean ± SD, n = 5, two-sided Mann-Whitney U test was used to calculate statistical significance, *p < 0.05 **p < 0.01 ***p < 0.001 (d) Representative flow cytometry gating strategy showing the Ki67 staining in CD19+B220+ Bc in Dura of naive (top row) vs. EAE mice at peak of disease (bottom disease). e, Quantification of the percentage of Ki67+ cells in the representative gates as shown D. Data represented as mean ± SD, n = 5 (c), n = 4 e, two-sided Mann-Whitney U test was used to calculate statistical significance, *p < 0.05 **p < 0.01 ***p < 0.001. f, Heatmap depicting the expression of gene signature (GSE28237) from follicular vs. early germinal center (GC) vs. late GC Bc in the Bc and cswBc cluster. Higher values mean higher overlap of the respective gene signature in cells located in the individual cluster.
