in an independent laboratory: an iPSC line generated by lentiviral integration of the OCT4, SOX2, NANOG and LIN28A genes into IMR90 lung fibroblasts (IMR90-iPSCs)5, and three iPSC lines generated by reprogramming of foreskin fibroblasts (FF) by non-integrating episomal vectors (FF-iPSC 6.9, FF-iPSC 19.7, FF-iPSC 19.11), as described previously7. We also sequenced the DNA methylome of the somatic FF progenitor line. Lastly, to study the effects of cellular differentiation on the DNA methylomes of ES cells and iPSCs, we differentiated cells of each to trophoblast lineage cells by growth in the presence of bone morphogenic protein 4 (BMP4)21. High-sequence coverage of the 11 new base-resolution DNA methylomes allowed interrogation of 75.7–94.5% of the genomic cytosines (Fig. 1a and Supplementary Table 1).
