Differential DNA methylation of human ESCs, iPSCs, and primary cells of various sources. These data show that iPSCs generated using our method from peripheral blood nonmobilized CD34⁺ cells have a general pattern of CpG methylation almost indistinguishable from ESCs and dramatically different from primary hematopoietic cells (CD14 monocytes, 3 separate samples of CD34⁺ cells, or mixed PBMCs) or the IMR-90 primary fibroblast line. The heat map encodes β values (red, methylated; blue, not methylated) of 2404 autosomal CpG sites (columns) and DNA samples (rows). The Illumina Infinium assay probed 485K methylation sites. Analysis of variance was used to test for a difference in average methylation level (β) between all pairs of 6 predefined classes of cells: ESCs (blue text), CD34⁺-derived iPSCs (green text), CD34⁺ cells (red text), PBMCs and CD14⁺ cells (pink text), and fibroblasts (black text). The CD34⁺-derived iPSCs include 13 independent lines from 9 different donors, 5 of which had the STEMCCA-loxP vector excised by Cre recombinase (iNC-01, iGP91-03-1, iGP91-03-2, iGP91-04, and iP47-02). We identified a total of 24 040 sites differentially methylated for at least 1 group comparison at a significance level of P < 1 × 10⁻¹²; 10% of those sites were selected at random for the subsequent cluster analysis of individual DNA samples. These methylation data are available under GEO accession number GSE40790.