Extended Data Fig. 1: Single-cell RNA-sequencing of the CNS macrophage niche.
(a) Dot plot depicting canonical cell-type-defining markers. Color scale: Relative expression level. (b) Bar graph showing the proportion of each cluster within the different tissues (Related to Fig. 2). (c) Marimekko chart showing the proportion of each cluster within each treatment group. CTL: control; 5d: five days after BLZ945; 8w: eight weeks after BLZ945. n = 4 (Dura 8w and 5d), n = 3 (Dura CTL), n = 8 (Leptomeninges and Cortex 8w and 5 d), n = 7 (Leptomeninges and Cortex CTL), arcsine transformation followed by ordinary one-way ANOVA combined with Benjamini–Hochberg FDR correction. (d) Violin plots showing expression levels of selected macrophage-niche factors and chemokines across niche cells. (e) Bar plot showing aggregated strength of all interactions at the different analysis time points. (f, g) Reclustered UMAP of all macrophage subsets in leptomeninges and cortex (f). Feature plots of condition (g, left) and Nes (Nestin) expression levels (g, right) are shown. Scale bar shows z-score of minimum to maximum scaled gene expression. (h) Dot plot depicting gene expression of a selection of tumor necrosis factor (TNF) signaling components and chemokines predicted to mediate interactions between myeloid and niche cells. Color scale: Relative expression levels.
