Extended Data Fig. 6: Effects of TLR9 genotypes on FO and MZ B cell gene programs.

RNA-seq analysis of sorted FO B cells (TCRβ⁻ CD19⁺ CD23^hi CD21^lo) and MZ B cells (TCRβ⁻ CD19⁺ CD23^lo CD21^hi) of the different Tlr9 genotypes from the 3-way BM chimera MRL/lpr mice (described in Fig. 6a), all over 19 weeks post-chimerization. a, PCA plot shows transcriptional differences between the FO B cells of the three genotypes Tlr9^WT, Tlr9^−/− and Tlr9^P915H, sorted from the 3-way BM chimera mice. b, Number of DEGs identified using Limma R package (Log2 fold-change >1 and FDR-corrected p value < 0.05) between the different Tlr9 genotypes from sorted FO B cells of the 3-way BM chimera MRL/lpr mice (n = 4 replicates). c, Venn diagram representing the number of up-regulated genes (from Fig. E6b), in Tlr9^WT FO B cells compared to Tlr9^P915H and Tlr9^−/− FO B cells. d, XY plot showing the DEG from Fig. E6b: (i) uniquely upregulated in Tlr9^WT FO B cells compared to Tlr9^−/− FO B cells; (ii) upregulated in Tlr9^WT FO B cells compared to Tlr9^P915H FO B cells; or (iii) upregulated in comparison to both Tlr9^P915H and Tlr9^−/− FO B cells. e, PCA plot showing transcriptional differences between the MZ B cells of the three genotypes Tlr9^WT, Tlr9^−/− and Tlr9^P915H, sorted from the 3-way BM chimera mice. f, Number of DEGs identified using Limma R package (Log2 fold-change > 1 and FDR-corrected p value < 0.05) between the different Tlr9 genotypes from sorted MZ B cells of the 3-way BM chimera MRL/lpr mice (n = 4 replicates). g, Venn diagram representing the number of up-regulated genes from Fig. E6f, in Tlr9^WT MZ B cells compared to Tlr9^P915H and Tlr9^−/− MZ B cells. h, XY plot showing the DEG from Fig. E6f): (i) uniquely upregulated in Tlr9^WT MZ B cells compared to Tlr9^−/− MZ B cells, (ii) upregulated in Tlr9^WT MZ B cells compared to Tlr9^P915H MZ B cells, or (iii) upregulated in comparison to both Tlr9^P915H and Tlr9^−/− MZ B cells.