Table S2). To investigate the extent to which iPSCs can retain the aging signatures of their donors, we performed high-throughput whole transcriptome RNA sequencing (RNA-seq) and compared the gene expression patterns of old and young fibroblasts and of derived iPSCs. The expression profiles of fibroblasts and iPSC samples were clearly distinguishable and clustered by overall expression similarity (Figure 1E). The independent clonal iPSC lines from the same donor typically, but not always, clustered together (Figure 1E). To identify putative aging genes, we performed differential expression analysis between cells derived from donors <40 years and cells from donors >40 years of age and found that, in fibroblasts, 78 genes were significantly differentially expressed, with a false discovery rate (FDR)-adjusted p value (padj) of <0.05 (Figure 1F; Table S3) (Benjamini and Hochberg, 1995). In contrast, iPSCs showed fewer overall expression variations and only one gene was determined to be significantly differentially expressed (Figure 1G). When only retrovirus-based iPSCs were compared, no genes were found to be significantly differentially expressed (data not shown). These data thus confirm that the age-dependent gene expression signatures present in primary fibroblasts become largely erased during reprogramming into iPSCs.
