Human iPSK3 cells are devoid of plasmid DNA. A) Southern blot analysis of genomic DNA from control iPS cells, iPSC6 and iPSC2 , generated by lentivirus transduction, human ES cells (H9, H9.14, and H9.15), or iPSK3 cells. DNA was digested with BamH1 and blots were hybridized with probes to detect FOXD3 as a loading control (left) or the puromycin N-acetyl transferase gene (right), which is present in both plasmid and lentiviral vectors. B) PCR analysis on total DNA extracted from either human ES cells (H9, H9.14 and H9.15), which lack exogenous DNA sequences, iPSC2 cells which contain integrated viral sequences, and iPSK3 cells using primers that specifically recognize the puromycin N-acetyl-transferase gene. PCR amplification without template DNA was performed to exclude DNA contamination. Primers that specifically recognize a human Alu sequence were used for loading control.