Extended Data Fig. 2: Subpopulations of microglia with distinct gene expression during development, in mice.

a, Distribution of Malat1 gene expression in a t-SNE plot (2,966 microglia cells). Colour keys represent the respective expression levels. The right cloud represents the embryonic microglial population, whereas the left cloud combines both juvenile and adult microglia as shown in Fig. 1a. b, Left, single-molecule fluorescent in situ hybridization (smFISH) for Malat1 and Cx3cr1 shows the kinetics of Malat1⁺ microglia during development. Scale bar, 10 μm. Representative images out of two adult mice investigated are shown. Yellow and white arrowheads indicate Malat1⁺Cx3cr1⁺ microglia and Malat1⁺Cx3cr1⁻ non-microglial cells, respectively. Right, frequency of Malat1⁺ microglia in the forebrain or cortex during development. Bar represents mean ± s.e.m. of 120 cells studied, from 3 animals per time point. c, t-SNE plot of Ctsd and Lamp1 gene expression; these genes were enriched in the C1 and C2 clusters, as shown in Fig. 1b. d, t-SNE plot of Eef1a1 and Rpl4 gene expression; these genes were enriched in the C6 cluster, as shown in Fig. 1b.