Gene expression markers and compositional differences in scRNA-seq datasets. (A, C, and E) Frequency of each population in scRNA-seq data from thymic epithelial cells (A), splenocytes (C), and salivary gland immune infiltrates (E). Each dot represents one animal. Data are presented as mean value with SEM and are obtained from one experiment with four Aire-deficient (KO) and three control (HE) rats per group for thymic epithelial cell and salivary gland immune infiltrate analysis and with three Aire-deficient (KO) and three control (HE) rats per group for splenocyte cell analysis. (B and D) Gene expression markers used for annotation of the splenocyte (B) and salivary gland (D) data. GD, gamma-delta; ILC, innate lymphoid cell; NK, natural killer; Teff, effector T cell; MZ, marginal zone; cDC, conventional dendritic cell, pDC, plasmacytoid dendritic cell.