Fig. 4: Region-dependent transcriptional dynamics of human CNS border macrophages during development.
From: Multiomic spatial landscape of innate immune cells at human central nervous system borders
a, Schematic overview of the included time points and compartments color coded for the studies from which immune-cell data were integrated with the present data. b, UMAP visualization of single-nucleus RNA-seq data from 59,053 single-nucleus transcriptomes generated for the present study, color coded for Seurat v.4 clusters. c, Single-cell heat map depicting the gene expression of the top 20 marker genes per cluster of the cells shown in b. Selected genes are shown on the left-hand side. Color coding of the clusters is consistent with b. The color scale represents Pearson’s residuals from a regularized negative-binomial regression. d, UMAP visualization of single-nucleus RNA-seq data for immune cells generated and integrated immune-cell data from published studies2,39. The colors indicate the results of graph-based re-clustering using Seurat v.4. e, Marimekko charts showing the cluster contributions of the macrophage populations from d to the respective time points. Each macrophage population is plotted separately. p.n., postnatal. The color coding is consistent with d. f, Volcano plots showing differential gene expression testing of ligand–receptor pairs of the indicated macrophage populations from d. Selected representative ligand–receptor pairs are highlighted. A two-sided unpaired Wilcoxon rank-sum test was performed with Bonferroni correction for multiple testing. The color scale represents an adjusted P value below 0.05 and a log2 fold change above 0.25. g, Volcano plots showing differential surface protein expression derived using CITE-seq from the indicated fetal macrophages at pcw 23 with their postnatal counterparts. A two-sided unpaired Wilcoxon rank-sum test was performed with Bonferroni correction for multiple testing. The color coding represents an adjusted P value below 0.05 and a log2 fold change above 0.25. h, Gene Ontology enrichment analysis between fetal and postnatal macrophages from g. Gene Ontology testing was based on the top 100 differentially expressed gene per cell type and time point. Dot sizes indicate the ratio of marker genes per cluster over the genes of a given terms. The color scales encodes the Benjamini–Hochberg-adjusted P value from a one-sided Fisher’s exact test.
