Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
MMLV retroviral insertion sites in ADS-iPSC genomic DNA were identified by an adapter ligation-mediated method for genome-wide mapping of insertions, as described previously (O'Malley 2007, Nature Protocols), except with the following modifications. Genomic DNA was fragmented by sonication with a Covaris S2, followed by ligation of modified 5 or 3 LTR-specific Illumina adapters (below) and PCR). 5-LTR (5-3): CCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTCAGTGCAGCTGTTCCATCTGTTCTTGGCCC 3-LTR (5-3): CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTCAGTGGCCAGTCCTCCGATTGACTGAGTCG Multiple libraries were sequenced in each lane, each with a unique barcode. Each valid read contained the barcode sequence “TCAGTG” prepended to the 5’ of the genomic DNA read sequence. SRR098045.1 contains the 5-LTR mapping library. SRR098046.1 contains the 3-LTR mapping library.