Panel A shows a stacked bar plot. The y-axis represents the fraction of cells, and the x-axis lists the experimental groups. Panel B is a bubble plot with bubble size representing gene count, and color indicates the normalized p-value. Panel C is a heatmap plot that uses a color scale to represent normalized RNA expression levels. Panel D is a scatter plot showing the mean fluorescence intensity of MHC 2 expression on various B cell populations in control and cKO mice at different ages. The y-axis represents the mean fluorescence intensity, and the x-axis represents the age in weeks. Panels E to K are bar graphs summarizing percentages and numbers of indicated cell populations from flow cytometry analysis of splenocytes, B cells, CD8 positive T cells, and MHC 2 expression on YFP positive and YFP negative B cells in the spleen of bone marrow chimeras. The y-axes represent percentages or numbers of cells, and the x-axes list the experimental groups. Panel L is a Kaplan-Meier survival curve showing the survival rates of bone marrow chimeras over time. The y-axis represents the survival percentage, and the x-axis represents time in months. Each symbol represents an individual mouse, and statistical significance is indicated.
scRNA-seq and functional analyses reveal that the cKO phenotype relies on CD4 + T cell interactions via MHC II. (A) Stacked bar plot summarizes fractions of main cell populations across four experimental groups: control total, cKO total, control YFP+, and cKO YFP+ samples in Fig. 3 A. (B) Bubble plot showing the top-ranked KEGG enriched terms among upregulated genes in main B cell subpopulations, based on GSEA comparing cKO and control YFP+ cells. The bubble size represents gene count of the enriched gene set, and color indicates the normalized P value. (C) Heatmap plot depicting RNA expression of the top-ranked DEGs in antigen processing and presentation pathway in cKO and control pre-GCB cells. The RNA expression level of each gene is normalized. (D) Statistical analysis of mean fluorescence intensity of MHC II expression on various B cell populations in control and cKO mice at indicated ages. (E–H) Flow cytometry analysis of splenocytes (E), B cells (F), CD8+ T cells (G), and MHC II expression on YFP+ and YFP− B cells (H) in the spleen of bone marrow chimeras in Fig. 3 G. Shown are bar graphs summarizing percentages and numbers of indicated cell populations. (I–L) Flow cytometry analysis of B (I) and CD4+ T cells (J and K) in the spleen of bone marrow chimeras in Fig. 3 I. Shown are bar graphs summarizing percentages and numbers of indicated cell populations. (L) Kaplan–Meier survival curves of bone marrow chimeras in Fig. 3 I. Each symbol represents an individual mouse. Small horizontal lines indicate the mean (±SD). Statistical significance is calculated using either one-way ANOVA followed by Tukey’s multiple-comparisons test (E–K) or the log-rank test (L). ns, not significant, P > 0.05; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. scRNA-seq data (A–C) from two independent biological replicates were merged for analysis. Two independent experiments (D–L) were performed.