Extended Data Fig. 5: TLR9 controls ABC gene programs independently of MyD88.

a, PCA plot showing differences in accessible regions between the ABCs of the three genotypes Tlr9^WT, Tlr9^−/− and Tlr9^P915H, sorted from the 3-way BM chimera mice. The different genotypes are represented as different shapes. b, PCA plot showing transcriptional differences between the ABCs of the three genotypes Tlr9^WT, Tlr9^−/− and Tlr9^P915H, sorted from the 3-way BM chimera mice. c, Venn diagram representing the number of up-regulated genes (from Fig. 7d), shared or unique between Tlr9^WT and Tlr9^P915H ABCs in comparison to Tlr9^−/− ABCs. d, Gene Set Enrichment Analysis (GSEA) was performed to look for plasma cell gene signature. GSEA shows significant enrichment of a plasma cell gene signature in Tlr9^WT compared to Tlr9^P915H ABCs (left panel), but no significant enrichment between Tlr9^WT and Tlr9^−/− ABCs (right panel). The p value was calculated using rankSumTestWithCorrelation function from the R limma package. e, XY plot showing the transcripts of the inhibitory pathway identified in Fig. 7d that were uniquely upregulated in Tlr9^P915H ABCs vs. the transcripts upregulated by both Tlr9^P915H and Tlr9^WT ABCs, compared to Tlr9^−/− ABCs. f, Quantification by qPCR (lower panels) of the transcripts of key inhibitory markers, found uniquely upregulated in Tlr9^P915H ABCs compared to Tlr9^WT and Tlr9^−/− ABCs by RNA seq (upper panels), in sorted Tlr9^−/−, Tlr9^P915H and Tlr9^WT ABCs from another cohort of 3-way BM chimera MRL/lpr mice (n = 4). g, Gene Set Enrichment Analysis (GSEA) was performed to look for TLR7-induced gene-set signature. GSEA shows no significant enrichment of TLR7-induced gene-set signature in Tlr9^−/− ABCs compared to Tlr9^P915H ABCs of the 3-way BM chimera MRL/lpr mice. The p value was calculated using rankSumTestWithCorrelation function from the R limma package. h, Venn diagram representing that only 20 genes were upregulated in Tlr9^−/− ABCs compared to both Tlr9^P915H and Tlr9^WT ABCs.

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