Supplementary Figure 9: SCENIC reveals the gene regulatory networks and master regulators that drive the transcriptional program of BAMs.

(a-c) SCENIC was performed on 10.947 brain macrophages pooled from the whole brain and border regions (see Fig. 2a). SCENIC yields AUC values per cell and per regulon which serves as a measure of the activity of a regulon in a cell (a) Binary activity matrix that predicts whether the indicated regulons are active (based on a regulon-specific AUC cutoff value) in individual cells. Black and white designate active and inactive regulons, respectively. Cells were clustered based on their regulon activity. The colors of the individual cells (shown at the top of the activity matrix) match the color of the clusters that were identified based on gene expression using Seurat (b top). Important regulons are shown for the various macrophage subsets: Microglia (orange), general BAMs (green), MHCII^lo BAMs (blue), MHCII^hi BAMs (red), CP^epi-BAM (pink) (b) tSNE plot based on gene expression (top) and tSNE plot based on the binary regulon activity matrix (bottom). Cells are colored based on their designation to the clusters in the expression-based tSNE. (c) AUC activity matrix that shows regulon activity using continuous AUC values from low (blue) to high (red). Cells are ordered per cell type on top with the colors matching the tSNE plot based on gene expression. Regulons are clustered based on their activity across cell types.