Extended Data Fig. 3: Validation of differential gene expression analysis.

a, Number of DEGs plotted against the total number of cells within the control and treatment groups. Each dot represents a DGE comparison of a cell type. b-d, Cumulative distributions of the calculated effect size (b), -log10(adj. p-value) (c) and log2 fold change values (d). Distributions are shown separately for ACC, REJ and AGE DGE. Vertical lines indicate the cutoffs applied throughout the study. e, Summary of ACC DGE results. Each cell type that has at least 50 cells in IY and HY is studied in the context of ACC and hence shown. From top to bottom: control and treatment sample sizes indicated separately for AGE and ACC, the number of genes differentially expressed in AGE and ACC, overlaps between AGE and ACC. Overlaps are normalized by the number of DEGs in the union of ACC and AGE DEGs. f, Summary of REJ DGE results. Each cell type that has at least 50 cells in IA and HA is studied in the context of REJ and hence shown. From top to bottom: control and treatment sample sizes indicated separately for AGE and REJ, the number of genes differentially expressed in AGE and REJ, overlaps between AGE and REJ. Overlaps are normalized by the number of DEGs in the union of REJ and AGE DEGs. g, Percent of DEGs that change in the same direction with AGE and ACC are plotted against the total number of DEGs within AGE and ACC for each comparison. Percentages are based on the union of DEGs as defined in (e) h, Percent of DEGs that change in the opposite direction with AGE and REJ are plotted against the total number of DEGs within AGE and REJ for each comparison. Percentages are based on the union of DEGs as defined in (f). i, Fraction of DEGs changing in the same direction with AGE and ACC plotted against the fraction of DEGs changing in the opposite direction with AGE and ACC. Each dot represents a cell type of the study. Colored area indicates where more DEGs change in the same direction than in the opposite direction. j, Fraction of DEGs changing in the same direction with AGE and REJ plotted against the fraction of DEGs changing in the opposite direction with AGE and REJ. Each dot represents a cell type of the study. Colored area indicates where more DEGs change in the opposite direction than in the same direction.