Differential expression analysis
Differential expression analysis for each cell type between different groups (YA and AA in cohort-1 and YH, AH, YCR and ACR in cohort-3) was performed using the t-test as implemented in the ‘‘sc.tl.rank_genes_groups’’ function of the Scanpy package. For each cluster, differentially-expressed genes (DEGs) were performed using the t-test and generated relative to all of the other cells. Before executing the differential expression analysis, we filtered out the cell types that were missing or had fewer than three cells in the comparison groups. An aging-associated and disease-related DEG dataset was established (adjusted P value < 0.05, |Log2FC| > 0.25) after identification of DEGs between AA and YA groups in cohort-1, AH and YH groups in cohort-3, ACR and AH groups in cohort-3, YCR and YH groups in cohort-3. The ‘‘upregulated DEGs during aging’’ were defined as the DEGs that increased in AA group and decreased in YA group. The ‘‘downregulated DEGs in aging’’ were defined as the DEGs that decreased in AA group and increased in YA group.