Extended Data Fig. 6: p52-ETS1 affects chromatin accessibility based on scATAC-seq in B cells.
From: The transcription complex p52–ETS1 is essential for germinal center formation
a-c, Splenic B cell subsets were sorted from Ctrl and p52ki/ki mice 9 days post NP-OVA and alum immunization for scATAC-seq. (a) Summary bar graphs of cell numbers for each B cell cluster identified from scATAC-seq from control and p52ki/ki mice on day 9 post NP-OVA and alum immunization (Fig. 4k). (b)Weighted kernel density plot presenting gene activity levels of Ighm and Ighd naïve B cells. (c) Top panel: Coverage plot illustrating normalized scATAC-seq sequencing tracks for Prdm1 gene across all clusters identified in (a). Bottom panel: Combined coverage plot across all clusters for the region in red box presented in upper panel. Two-tailed wilcoxon rank-sum statistical test with adjustment for multiple comparisons correction was used to analyze data, adjusted p ≤ 0.05. d-f, Ctrl and p52ki/ki were immunized with NP-OVA and alum intraperitoneally before expression of markers of proliferation and apoptosis on GC B cells (CD19+ IgD− Fas+ GL7+) were assessed by flow cytometry on day 9. (d) Summary bar graph of frequencies of Ki-67+ cells within splenic GC B cell population. (e) Representative flow cytometry plots and summary bar graphs of (f) frequencies of active caspase 3+ (aCasp3) cells within splenic GC B cell population from Ctrl (n = 9) and p52ki/ki (n = 10) mice. Pooled data from 3 independent experiments, minimum n = 3 mice per group. d,f, Data are presented as mean ± sd with each data point representing biological sample from an individual mouse. Statistical analyses were performed using two-tailed Mann-Whitney U-tests in (d, f). Mice were sex matched per experiment. Both male and female mice used in these experiments were 8-12 weeks old.
