Identification of GC B cell subpopulations by sc-RNAseq and CITE-seq in distinct donors. Related to Fig. 1. (A) Representative counterplots and gating strategy from cytofluorimetric analysis of human GC (CD3⁻/IgD⁻/CD38⁺), DZ (CD3⁻/IgD⁻/CD38⁺/CD83^lo/CXCR4^hi), and LZ (CD3⁻/IgD⁻/CD38⁺/CD83^hi/CXCR4^lo) B cells isolated from tonsil tissue are shown. (B) Overview of the computational steps used to analyze sc-RNAseq data indicating the software tools used (black labels). (C) UMAP projection of 4,759 GC B cells (CD3⁻, IgD⁻, CD38⁺) isolated from Donor 1. Cells are colored by clusters identified by PhenoGraph and assigned to one of the following groups: DZ, intermediate (INT), LZ, PreM, or PBL. UMAP projections colored by the z-scored expression of CXCR4 (DZ), CD83 (LZ), CCR6 (PreM), and PRDM1 (PBL) are displayed below. (D) UMAP projection of 3,609 GC B cells (CD3⁻/IgD⁻/CD38⁺) isolated from Donor 2. Cells were clustered and colored using the same methods as for Donor 1. Below, the same gene expression markers described for Donor 1 are shown for Donor 2. (E) CITE-seq analysis of 8,871 GC B cells (CD3⁻, IgD⁻, CD38⁺) isolated from Donor 3. Left: UMAP projection based on mRNA data. Cells were clustered and colored using the same methods as for Donors 1 and 2. Right: UMAP projections colored by normalized z-scored mRNA expression (top) and center log ratio normalized protein expression (bottom) as measured by ADTs for selected markers (CXCR4, CD83, CD9, CCR6, CD69, and CD44).