Figure S4.

Spp1 inactivation transiently alters CSA and CSB integrity, related to Figure 5

(A) Dot plot reporting the average expression level of Spp1 and Gpnmb in various cell types of La Manno et al.³⁰ scRNA-seq data across different embryonic time points (229,948 cells). Color represents the average expression level across all cells within a cluster, while the dot size indicates the percentage of cells expressed in that cluster.

(B) E14.5 coronal hemisection stained with Hoechst, showing the integrity of the CSA in control mice and Gpnmb^−/− mutants (open arrowheads) (n_controls = 18, n_GpnmbKO = 13, from at least 2 distinct litters).

(C) L1 immunolabeling showing the integrity at the CSB in control mice and Gpnmb^−/− mutants (open arrowheads) (n_controls = 23, n_GpnmbKO = 8, from at least two distinct litters).

(D) CSA and CSB lesions in Spp1^−/− mutants are transient and have resorbed, respectively, by E18.5 (n_controls = 9; n_Spp1KO = 3, from at least 2 distinct litters) and P3 (n_controls = 6; n_Spp1KO = 4, from at least two distinct litters). Graphs show the percentages of brain with lesions, but individual dots represent brains with lesion (100) or no lesion (0), to illustrate sample numbers.

(E) UMAP visualization of all sorted cells (from wild-type [WT] and Spp1^−/− E14.5 and E18.5 embryos) colored by annotated clusters (BroadCellType).

(F) UMAP of all sorted cells split and colored by WT (light gray) and Spp1^−/− (dark gray) conditions.

(G) Dot plot of scaled average expression and percentage of top 5 differentially expressed genes (DEGs) by annotated macrophage clusters (RefinedCellType).

Scale bars, 200 μm.

ATM, axon-tract associated microglia; BAM, border associated macrophages; CC, corpus callosum; CSA, cortico-striato-amygdalar boundary; CSB, cortico-septal boundary; Fx, fornix; Ncx, neocortex; MG, microglia; PVM, perivascular macrophages; Se, septum; Str, striatum; WT, wild-type.