Phenotypic and functional changes in Mrc1 ^Cre Xpr1 ^fl/fl animals. (A) Violin plots showing the expression of Mrc1 in the indicated clusters of E15.5 FL cells. Data refer to scRNA-seq data in Fig. 3 A. (B) Immunohistochemistry of E15.5 Xpr1^fl/fl control liver stained for IBA1 (cyan), CD206 (magenta), and CD31 (white). Insets: Single stainings shown of the outlined region in the overview image. Scale bar: 100 µm, inset 50 µm. Filled arrowheads show CD206⁺ macrophages, open arrowheads show CD206⁺ endothelial cells. (C) Representative flow cytometry plot of CD206 expression in liver macrophages extracted from E15.5 Xpr1^fl/fl embryos (pre-gated on CD45⁺CD31⁻Ly6G⁻F4/80⁺CD11b⁺TER119⁻ cells). (D) Representative flow cytometry plots of Tim4 expression in liver macrophages extracted from E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl embryos (pre-gated on CD45⁺Ly6G⁻F4/80⁺ cells). Data are representative of at least n = 5 per group. (E) Representative flow cytometry plots and graph showing the percentage (normalized to control) of pHrodo Red⁺ FL macrophages (gated on CD45⁺F4/80⁺CD11b^int cells) from Mrc1^CreXpr1^fl/fl and Xpr1^fl/fl FLs at E15.5, exposed in vitro to pHrodo Red Zymosan bioparticles for 90 min. Data shown are n = 3–6 per group and are pooled from two independent experiments. Statistical analysis was performed using the Student’s t test. (F) Heatmap of all 6,208 DEGs in the RNA-seq data of Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages from Fig. 5 E. Genes indicated are the core KC-genes and KC-associated transcription factors identified in Bonnardel et al. (2019). (G) Gene ontology analysis for biological processes of the DEGs in the RNA-seq data of Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages from Fig. 5 E. (H) Representative flow cytometry plots, frequencies, and numbers (mean ± SD) of Tim4 expression on KCs of adult Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl mice (pre-gated on CD45⁺Ly6G⁻F4/80⁺ cells). Data shown are n = 3–5 per group and are pooled from two independent experiments. Statistical analyses were performed using the Student’s t test. (I) Representative flow cytometry plots, frequencies, and numbers (mean ± SD) of KCs of adult Xpr1^fl/fl and Siglec1^CreXpr1^fl/fl mice (pre-gated on CD45⁺Ly6G⁻F4/80⁺ cells). Data shown are n = 3 per group. Statistical analyses were performed using the Student’s t test. (J–M) Representative flow cytometry plots, frequencies, and numbers (mean ± SD) of (J) heart macrophages (Heart Macs) (pre-gated on CD45⁺Ly6G⁻ cells), (K) Langerhans cells (LCs) (pre-gated on CD45⁺Ly6G⁻TCRβ⁻SiglecF⁻Langerin⁺ cells), (L) kidney macrophages (Kidney Macs) (pre-gated on CD45⁺Ly6G⁻CD3⁻CD19⁻B220⁻CD49b⁻CD90⁻ cells), and (M) alveolar macrophages (AMs) (pre-gated on CD45⁺Ly6G⁻CD3⁻CD19⁻B220⁻CD49b⁻CD90⁻ cells) of adult Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl mice. Data shown are n = 5 per group and are pooled from two independent experiments. Statistical analyses were performed using the Student’s t test. *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. ns, not significant.