Extended Data Fig. 5: ATAC–seq of TFH and non-TFH populations from multiple genetic backgrounds.

Related to Fig. 5 a, Representative flow cytometry of naive SMARTA cells (CD44^loCD62L^hiCD45.1⁺) used for ATAC–seq analysis. b, Genome-browser tracks depict ATAC–seq chromatin accessibility at Cxcr5 locus. Peak calls indicated below each track. * indicates DEseq2 raw p ≤ 0.05 in comparison between WT T_FH and T_H1. c, Genome-browser tracks depict ATAC–seq chromatin accessibility at Tbx21 and Gata3 loci. Peak calls indicated below each track. Bcl-6 liftover peaks from human to mouse reference genome are indicated. * and ** indicate DEseq2 raw p-val ≤ 0.05 and ≤ 0.01, respectively, in comparison between WT T_FH and T_H1. Gene expressions from RNA-seq data of LCMV_Arm infected mice are graphed. DKO, Bcl6^f/fPrdm1^f/f Cre^CD4. d, Genome-browser tracks depict BCL-6 ChIP–Seq peaks at SELPLG locus. Peak calls indicated below the track. e, Representative flow cytometry and quantification of the level of Bcl-6 in RV⁺ T_FH or non-T_FH SMARTA cell subsets from spleen of LCMV_Arm infected mice. SMARTA CD4 T cells transduced with GFP-RV or Bcl6-RV were transferred to C57BL/6 host mice, followed by infection of the host mice with LCMV_Arm, and analyzed 3 days after infection. Non-T_FH: GFP-RV⁺ and T_FH: GFP-RV⁺ indicate the expression level of endogenous Bcl-6 in each population. Each dot represents one mouse (n = 4). Data are mean ± s.d., unpaired two-tailed Student’s t-test. f, Representative flow cytometry and quantification of GC-T_FH and B_GC subpopulations from spleen of LCMV_Arm infected mice. Bcl6^f/f Cre^CD4 SMARTA CD4 T cells transduced with Bcl6-RV or myctagN-Bcl6-RV were transferred to Bcl6^f/f Cre^CD4 host mice, followed by infection of the host mice with LCMV_Arm, and analyzed 8 days after infection. We validated that an myctagN-Bcl6-RV was functionally comparable with non-tagged Bcl6-RV (Bcl6-RV), based on myctagN-Bcl6-RV rescue of T_FH differentiation and B cell help function of Bcl6^f/f Cre^CD4 CD4 T cells in LCMV infected mice. Each dot represents one mouse (n = 4). Data are mean ± s.d.