Fig. 4
From: Commensal microbiota drive the functional diversification of colon macrophages
Colon MP diversification from CCR2+ common precursors. a Developmental trajectory analysis of colon macrophages (cluster 1, 2, 3, 4, 6, 7, 11 from scRNA-seq data) with pseudo-time (left panel) and cell cluster identity (right panel). Cluster 1 (red: Ccr2+), 4 (green: Il1r2+), and 6 (blue: Mrc1hi) and 7 accumulated at pre-branch, cell fate 1 and cell fate 2, respectively. b Dynamic change of expression of MP maturation markers (Adgre1, Cd63, Cx3cr1 and Ccr2) along the pseudo-time. c Principal component analysis (PCA) of gene expression using bulk RNA-seq of P1–P8 populations sorted from steady state colon defined as in Supplementary Fig. 5a-c. Samples from SPF (•) or GF (▴) mice. P3 (red), P6 (green), and P7 (blue) are the counterparts of cluster 1 (red: Ccr2+), 4 (green: Il1r2+), and 6 (blue: Mrc1hi) from scRNA-seq data, respectively. d Heatmap displaying top50 genes of determining the variance of PC1 or PC2, and MP maturation markers. Genes highlighted in red represent the genes that are also highly expressed in the corresponding cell subsets from scRNA-seq data. Subset-specific genes are in black dotted boxes. Blue dotted box highlights the transitional expression pattern of PC1 genes from monocytes to MPs. First two and later two in each subset (P1–P8) are from SPF and GF, respectively.
