Extended Data Fig. 3: Molecular and topological identity of light and dark zone FDC at a single cell level.

a, b, Strategy for demarcating distinct regions of the B cell follicle for topological BRC analysis using positioning, TdTom fluorescence intensity, and IgD and CD21/35 immunostaining. Each dot in (b) represents one cell body, color-coded according to the occupied region in the follicle. Scale bars, 100 μm. c, BRC enumeration per region of B cell follicle. d, Quantification of the mean fluorescence intensity (MFI) of TdTom in each region of the B cell follicle (according to color-code). e, f, Merged images and single channels corresponding to Fig. 3c,d. Scale bars, 100 μm. Images are representative of at least two mice per condition. g, Confocal microscopy analysis of IgD, TdTom, CD21/35 and MYH11 staining in secondary B cell follicles of Cxcl13-Cre/TdTom EYFP mice. Images are representative of at least 5 immunized Cxcl13-Cre/TdTom mice. (c, d). N = 7 naïve Cxcl13-Cre/TdTom mice, 3 independent experiments, N = 5 VSV-immunized Cxcl13-Cre/TdTom mice, 2 independent experiments. Mean and SEM are depicted. P values as per one-way ANOVA with Tukey’s multiple comparisons test.