Library construction for deep sequencing of iPSCs and myoblasts

Library construction for deep sequencing was performed using a modified version of our previously described protocol^{26 (link)}. Briefly, iPSCs and myoblasts were harvested following nuclease treatment and genomic DNA was extracted with the GenElute Mammalian Genomic DNA Miniprep Kit (Sigma G1N350). Genomic loci spanning the target sites were PCR amplified with locus-specific primers carrying tails complementary to the TruSeq adapters (Deepseq_TCAP_primer_fwd & Deepseq_TCAP_primer_rev; Supplementary Table 8). 50 ng input genomic DNA was PCR amplified with Q5 High-Fidelity DNA Polymerase (New England Biolabs): (98°C, 15s; 67°C 25s; 72°C 20s) x30 cycles. Next, 0.1 μl of each PCR reaction was amplified with barcoded primers to reconstitute the TruSeq adaptors using the Q5 High-Fidelity DNA Polymerase (New England Biolabs): (98°C, 15s; 67°C, 25s; 72°C, 20s) x10 cycles. Products were qualitatively analyzed by gel electrophoresis. Equal amounts of the products were pooled and gel purified using QIAquick Gel Extraction Kit (Qiagen Cat. #28704). The purified library was deep sequenced using a paired-end 150bp Illumina MiSeq run.