Figure S4.
scRNA-seq. (A) UMAP displaying the expression of different cell markers to identify cell types. (B) Antigen presentation signature projected on the UMAP. (C–F) Volcano plot of DEGs between NIKΔCX3CR1 (n = 4) and control (n = 4) in the resDC2 subset, (D) Ly6Chi monocyte subset, (E) Cxcl10 monocyte subset, and (F) Ly6Clo monocyte subset. Left are genes downregulated in NIKΔCX3CR1, and right are genes upregulated in NIKΔCX3CR1. Genes on the X or Y chromosome, ribosomal genes, and low-reproducibility genes were excluded from labels. (G) KEGG pathway enrichment analysis was performed on DEGs (adjusted P < 0.05 and |log2 fold change| >0.1 and less than −0.1) from the combined monocyte clusters (Ly6Chi/Ly6Clo/Cxcl10). The dot plot shows enriched pathways ranked by significance. Each dot represents a KEGG pathway. Circle size = count of DEGs found within each pathway; color = adjusted P value. Refer to the image caption for details.

scRNA-seq. (A) UMAP displaying the expression of different cell markers to identify cell types. (B) Antigen presentation signature projected on the UMAP. (C–F) Volcano plot of DEGs between NIKΔCX3CR1 (n = 4) and control (n = 4) in the resDC2 subset, (D) Ly6Chi monocyte subset, (E) Cxcl10 monocyte subset, and (F) Ly6Clo monocyte subset. Left are genes downregulated in NIKΔCX3CR1, and right are genes upregulated in NIKΔCX3CR1. Genes on the X or Y chromosome, ribosomal genes, and low-reproducibility genes were excluded from labels. (G) KEGG pathway enrichment analysis was performed on DEGs (adjusted P < 0.05 and |log2 fold change| >0.1 and less than −0.1) from the combined monocyte clusters (Ly6Chi/Ly6Clo/Cxcl10). The dot plot shows enriched pathways ranked by significance. Each dot represents a KEGG pathway. Circle size = count of DEGs found within each pathway; color = adjusted P value.

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