Fig. 2

Transcriptome and pathway analyses of FO and MZ single-κ and dual-κ B cells (a) RNASeq analysis of FO (left) and MZ (right) single and dual-κ B cells, sorted from spleen cells pooled from N = 2–4 mice for each biological replicate. Sorting strategy is described in Supplementary Fig. 2a. Heat maps display differentially expressed genes (FDR ≤ 0.05) between single-κ and dual-κ B cells of FO (1938 genes) or MZ (446 genes) cell subsets. The maps represent min/max row-scaled rlog values, where the expression values are mapped to colors using the minimum and maximum of each row/gene independently. b Differential expression of Cd19, Cd79A, and IgκV genes from RNAseq data described in a displayed as mean log2-fold change ± SEM in dual over single-κ cells for each group. The values for IgκV genes were calculated as the mean log2-fold change (±SEM) of all IgκV genes with FDR ≤ 0.05, which were N = 14 in FO and N = 30 in MZ cells (represented by symbols on the graph). A log2 value of zero indicates equal expression, while a value of 1 indicates a 2-fold difference. c Differential expression (mean for each group of the log2-fold change ± SEM) of Jκ genes in FO or MZ dual-κ relative to single-κ B cells. d B cell-relevant pathways identified by Ingenuity Pathway Analysis (IPA) as differently activated (based on FDR ≤ 0.1) in FO (top) and MZ (bottom) dual-κ B cells relative to single-κ B cells. Vertical dashed lines indicate the 0.05 -log(p-value) above which the pathway is considered significantly enriched. Data analysis was performed using DESeq2 and significance was assessed by the Wald test with the Benjamini and Hochberg adjustment. Data in all panels are from three independent biological replicates analyzed in one experiment