Fig. 5. Transcriptomic profiling analysis of clusters of Xeno MG and mouse microglia.

a tSNE plot highlighting only the clusters of human Xeno MG and mouse host microglia. b Scatter plot showing mean mRNA expression levels of human and mouse genes with unique orthologs from Xeno MG and mouse microglia clusters, highlighting the differentially expressed genes (DEGs; at least twofold different) in human Xeno MG (red) or mouse microglia (green) from 6-month-old chimeric mouse brain. Significantly different DEGs (<5% false discovery rate (FDR) and at least twofold different) are listed in Supplementary Data 2. c Violin plots summarizing expression differences in individual cells within the human Xeno MG and mouse microglia clusters. Dots indicate expression levels (as log normalized counts) of individual cells and the violin shape summarizes the distribution of expression in the population. d Bar plots showing the average expression (mean ± SEM, n = 4 samples) of Multiple sclerosis (MS)-associated genes in Xeno MG and mouse microglia. These genes were reported to be differentially expressed between human and mouse microglia as in Gosselin et al.⁷. Source data are provided as a Source Data file. e Venn diagrams showing that majority of the MS associated genes that were reported to be differentially expressed between human and mouse microglia are recapitulated in our chimeric mouse model (29 of 32).