Extended Data Fig. 1: Outline of data analyses and tissue specific data overview.

a, Outline of computational analyses. Single-cell count data are processed per tissue, see Methods ‘Quality control’-’Cell type annotation’. Differential gene expression is then conducted per cell type and comparison (AGE, ACC, REJ) within each tissue, see Methods ‘Differential gene expression’. All of the next panels present data after quality control. b, Number of cells per tissue and replicate. Replicates are colored by their condition. c, Number of replicates per tissue. Replicates are colored by their condition. d, Total number of cells per tissue. e, Fraction of cells within each condition per tissue. f-i, For each experimental condition within each tissue: total read counts (f), the percent of reads mapped to ribosomal genes (g), mitochondrial genes (h), and ERCC spike-ins (i) plotted against the mean number of genes expressed. j, Average LISI scores of mouse replicates calculated over the batch corrected tissue specific UMAP embeddings plotted against the mean LISI scores of tissue specific UMAP embeddings calculated from neighborhood graphs without batch correction. k, Mean entropy batch mixing of mouse replicates calculated over the tissue specific batch-corrected neighborhood graph plotted against the mean entropy batch mixing calculated from neighborhood graphs without batch correction. l, Result of saturation analyses shown per condition (Y, A, IY, HY, IA, HA). Downsampling was carried out per condition within each tissue separately. Results indicate the number of detected genes as the function of the downsampled total counts.