Variable mRNA expression, CNV, and growth of iPSC lines from the same and different fibroblast source. (A) Representative FACS purification of human iPSCs (or ESCs) expressing high levels of pluripotency markers SSEA3 and Tra-1-81. Presorted culture (left) gated at a high level of SSEA-3/TRA-1-81 expression and purity analysis of postsorted cells. (B) mRNA expression analysis of sorted iPSCs and ESCs. (i) PCA representation of gene expression variations across individuals and within the same individual: CHOPWT1 (black), CHOPWT2 (red), BMC (green), and ESCs (blue) and (ii) comparison of gene expression from CHOPWT2 cell lines. The heat map shows the expression of 25 upregulated and 25 downregulated genes between the WT2 cell lines, criteria Student t test (P < .05), and at least a 1.5-fold change. Genes were ordered according to decreasing average expression ratio. Quantitative real-time PCR plots of BCLX and 2 examples of genes that were either upregulated or downregulated in WT2.1 compared with WT2.2 and WT2.3 iPSC lines (*P < .05 and **P < .01). Data are presented as relative expression compared with the CHOPWT2.1 expression level. (C) Total number of genes acquired or deleted during the reprogramming process for each iPSC line established. (D) Seven-day cell expansion of undifferentiated iPSC lines: CHOPWT1 (green), CHOPWT2 (blue), BMC (red). iPSC expansion expressed as fold change above starting cell numbers. Data are representative of 3 experiments (mean ± SEM, *P < .05).