Figure 3. Transcriptomic profiling of Cx3cr1⁺ and Cx3cr1^neg i-OCLs reveals two distinct populations of i-OCLs.

(A) Schematic representation of the differentiation of GFP⁺ (Cx3cr1⁺) and GFP^neg (Cx3cr1^neg) i-OCLs from BM-derived DCs of WT Cx3cr1^GFP/+ mice and their sorting (gated as in Figure 2—figure supplement 1). (B) Principal component analysis of Cx3cr1⁺ and Cx3cr1^neg i-OCLs clusters samples in two groups (red: GFP⁺ (Cx3cr1⁺) OCLs and blue GFP^neg (Cx3cr1^neg) OCLs, both from Cx3cr1^GFP/+ mice). Data shows the two first components on the top 500 most differentially expressed genes after batch correction. Each dot represents the expression profile of one sample. (C) Volcano-plot showing representative differentially expressed genes for Cx3cr1⁺ and Cx3cr1^neg i-OCLs. Cut-off values were defined by a fold change (FC) >2 and an adjusted p-value<0.05. (D) Heatmap visualization of the top 107 genes significantly differentially expressed between GFP⁺ (Cx3cr1⁺) and GFP^neg (Cx3cr1^neg) i-OCLs from Cx3cr1^GFP/+ mice (adjusted p-value<0.05, FC ≥2). (E) Graphical representation of gene ontology analysis associated with differentially expressed genes between Cx3cr1⁺ and Cx3cr1^neg i-OCLs.

Figure 3—figure supplement 1. Cx3cr1⁺ and Cx3cr1^neg i-OCLs differ in their expression of Cx3cr1-interacting genes.

(A) Heatmap visualization of selected genes involved in the Cx3cr1 pathway that are significantly differentially expressed (p<0.05, FC ≥2) between GFP⁺ (Cx3cr1⁺) and GFP^neg (Cx3cr1^neg) i-OCLs differentiated from WT Cx3cr1^GFP/+ mice. (B) Relative expression levels of Nr1d1 and (C) Tlr4 in Cx3cr1⁺ and Cx3cr1^neg i-OCLs. (D) BM-derived DCs from Cx3cr1^GFP/+ mice were sorted based on their expression of GFP and were differentiated into i-OCLs. Both GFP⁺ (Cx3cr1⁺) and GFP^neg (Cx3cr1^neg) DCs gave rise to approx. 20% of Cx3cr1⁺ i-OCLs. *p<0.05; ****p<0.0001.