Panel A: U M A P plot showing distribution of macrophage populations based on C d 4 expression levels. Panel B: U M A P feature plots showing expression patterns of C D 163 positive and negative subsets across C d 4 negative and positive macrophage populations. Panel C: Heatmaps showing differential gene expression across macrophage subsets, highlighting pathways related to cytoskeletal regulation and inflammatory signaling.
Gene set pathway analysis for cluster 4. (A) UMAP plot showing expression levels of Cd4. (B) UMAP plots showing cells expressing genes from sorted CD163− and CD163+ subsets of Tim-4−CD4−, Tim-4−CD4+, and Tim-4+CD4+ macrophages of the small intestine of WT mice overlaid onto scRNA-seq data from live CD45+Lin−CD11b+MHCII+CD64+ cells from the small intestine of WT and Ccr2−/− mice. (C) Heatmaps showing expression profiles of genes in the top two pathways identified by PANTHER pathway analysis for cluster 4. (B and C) CD163− and CD163+ subsets of Tim-4−CD4−, Tim-4−CD4+, and Tim-4+CD4+ macrophage of the small intestine were isolated by FACS from five pooled 8–10-wk-old C57BL/6 WT mice, from at least three independent sorts, for bulk RNA-seq. UMAP, uniform manifold approximation and projection.