Variation between iPSC lines has been attributed to many factors, such as cell type of origin, donor, culture conditions, and reprogramming method. To perform unambiguous studies on retention of cell-type memory, we generated isogenic iPSC lines from fibroblasts (F-iPSCs) and PBMCs (B-iPSCs) by Sendai virus-mediated reprogramming under standardized conditions (Figure 1A and Table 1) (Nishimura et al., 2011, Trokovic et al., 2014). To reduce gender-associated variation, only female donors were selected for the study. All iPSC lines expressed stem cell markers and showed morphology and growth characteristics similar to those of hESCs, and were propagated up to passage 9–17 (Figures S1A and S1B; Table 1). All iPSC lines were able to spontaneously differentiate into three embryonic germ layers in embryoid bodies (Figure S1C). To avoid the confounding effects of partially reprogrammed cells, only cell lines identified as bona fide iPSCs by PluriTest (Muller et al., 2011) were selected for further experiments (Figure S1D). To avoid batch effects in expression profiling (Leek et al., 2010), we distributed F- and B-iPSC lines across batches (Table 1). Global gene expression analysis of all
