To explore our hypothesis that fibroblast-derived iNs retain information about their donor’s age, we performed RNA-seq analysis of iNs FACS-purified at 3 weeks of conversion (n = 22 samples from 18 donors). Unsupervised hierarchical clustering based on overall gene expression showed high similarity between all iN samples, and independently repeated iN conversions from the same fibroblasts reliably clustered together (Figure 4A). Strikingly, differential expression analysis between young (<40 years) and old (>40 years) fibroblasts and iNs revealed profound age-dependent gene expression in the iNs, with 202 genes significantly differentially expressed (FDR < 0.05; Figures 4B and 4C). In addition, linear correlation of normalized gene expression values with donor age confirmed that both fibroblasts and iNs showed a subset of genes progressively increasing or decreasing with age (Figure S3). Surprisingly, only seven of the differentially expressed genes overlapped between fibroblasts and iNs, as both cell types appeared to show cell-type-specific, age-dependent expression profiles (Figure 4D; Table S3). GO term and KEGG pathway analysis revealed that, in fibroblasts, genes involved in wound healing, stress response, and Ca2+ signaling—which are categories that have
