Figure S3.

FDC volcano plots and microscopy. (a) Volcano plots of different cluster combinations. Top 10 genes are labeled. Significant differential expressed genes are colored orange (down) or blue (up). Dotted line indicates twofold log change. (b) Images of the full follicle to assess outside follicle background. Scale bars, 40 µm. (c) Additional fluorescent microscopy staining of human tonsil sections. Scale bar, 10 µm. (d) Pearson’s correlation of markers with CD35 by microscopy. Quantification corresponds to Fig. 2 c. Within a follicle region of interest, the colocalization between CD35 and the corresponding marker was calculated by Pearson’s correlation. (e) Percentage of follicles with CD14, CD23, or CD21. After thresholding, positive and negative follicles were counted by hand. Example of CD23 tonsil slice after threshold. Scale bars, 1 mm; insert, 100 µm. scRNaseq data, n = 4; microscopy data, n = 3 (biological replicates); Pearson’s correlation, n > 3 (biological replicates).