Karyotyping analysis by standard G-banding technique was carried out by the Cytogenetics Core Facility at the Johns Hopkins Hospital or Cell Line Genetics. Results were interpreted by clinical laboratory specialists of the Cytogenetics Core or Cell Line Genetics. Genotyping analysis was performed as described previously16. Genomic DNA of fibroblasts and derived iPS cells was extracted by DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s recommended protocol. Apair of specific primers was used to amplify the region around the 4-bp deletion (Supplementary Table 1c). PCR products were cloned by TA cloning and sequenced. Bisulphite genomic sequencing was carried out with the EZ DNA Methylation-Direct Kit (Zymo Research) as previously described32. After bisulphite conversion of genomic DNA from iPS cells, primers specific to human OCT4 and NANOG promoters (Supplementary Table 1c) were used to amplify genomic DNA sequences with Platinum Taq DNA Polymerase High Fidelity (Invitrogen) for sequencing.
