a) Cell signatures of microglial and non-microglial cells. Aggregate transcript counts of genes enriched in the given cell type (indicated in parentheses) are color-coded on t-SNE maps. b) Unsupervised clustering of microglia after exclusion of non-microglial cells divided microglia in 9 major populations, that is clusters. The heatmap displays pairwise cell-to-cell distances with clusters color-coded on the bottom. C4 (grey color) was removed from subsequent analysis due to upregulation of cell-stress genes indicating dissociation-induced artefacts. Minor clusters containing individual cells that comprise less than 1 % of all cells were also removed (white ‘x’ on black background), leading to n = 4,116 microglia that passed quality control. The color scale represents the pairwise distance between cells.