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 cell lines showed that pluripotent stem cells (PSCs) clustered together and were clearly separated from their parental cell lines (Figures 1B and S1E). Expression analysis of genes located in X chromosome showed little variation between lines (Figure S1F), suggesting that our female iPSC lines retain an inactive X chromosome (Tchieu et al., 2010). Global DNA methylation analysis performed at a single-nucleotide level using reduced representation bisulfite sequencing (RRBS) (Meissner et al., 2005) also resulted in a clustering of PSCs (Figure 1C). Interestingly, both global DNA methylation and gene expression analyses revealed a tendency of iPSC lines to cluster according to the donor rather than cell type of origin (Figures 1C and S1E).
