To get a more global impression of the impact of CD83-deletion on microglial function during homeostasis and neuro-inflammatory conditions, we next performed single-cell RNA sequencing (scRNA-Seq) analyses on microglia sorted from the brains of healthy and EAE CD83ΔMG and control mice, respectively. The workflow of these experiments is shown in Fig. 4a. Briefly, microglia were isolated from both strains, either from naïve mice or at the peak of EAE (day 16 after induction). Then, we employed a droplet-based RNA-Seq approach with four animals per genotype and condition. After initial quality control, integration, and removing clusters of potentially contaminating T cells and macrophages (Supplementary Fig. 5a, b), single-cell transcriptomic profiles for 20,901 cells and 15,984 genes were selected for the analysis. Unsupervised clustering of cells was performed using Seurat’s graph-based clustering, and cells were projected on a Uniform Manifold Approximation and Projection (UMAP) to visualize clustering (Fig. 4b). We obtained six clusters, two of which were associated with cells from healthy animals (Gpr34+ and Ccl4+) while the other four cluster largely contained cells from EAE animals (Fig. 4c). Cells in the
