Fig. 6: BL/6 and BALB/c cell intrinsic responses to IL-4 activation in the mixed bone marrow chimeras F1 mouse.

a Schematic illustration of the experimental protocol: Bone marrow (BM) cells from BL/6 and BALB/c mice were adoptively transferred into F1 mice. After 8 weeks, chimeric mice received two i.p. injections of 10 µg IL-4-Fc per mouse. Peritoneal cells were harvested 4 days after the first injection for scRNA-seq library construction. b UMAP plots visualized clusters of peritoneal cells derived from scRNA-seq of chimeric F1 mice. The clusters were color-coded based on their annotated cell names. The subset of macrophages was isolated for further analysis. c Feature plots show the selected genes expression of BL/6 and BALB/c macrophages. d Dot plots visualizes genes more expressed in BL/6 macrophages, of which Trem2, Sgmas1, Per3, Zmiz1, and Mertk have NF-κB motifs in the promoter-distal regions defined by chromatin loops from Hi-C data. Red indicates a higher average expression of the gene, and a larger dot size indicates that the gene is present in a larger percentage of cells within that cluster. e Regulons activities were computed for macrophages using SCENIC. The regulon names are labeled on the right side of the figure, with the red color-labeled names highlighting the SDTFs related regulons in BL/6 mice. f UMAP plots display the integration of scRNA-seq and scATAC-seq data. The subset of macrophages was isolated for further analysis. g, h SCENIC+ analysis was performed after integrating scRNA-seq and scATAC-seq datasets. Cytoscape visualization of separate eGRNs formed by Stat5a, Stat2, Spib, and E4f1 in BL/6 TRMs after IL-4 treatment (g), and the eGRN formed by Meis1, Bach2, Zfp202, and Ikzf3 in BALB/6 TRMs after IL-4 treatment (h).