Additional Supporting Information may be found in the online version of this article.

STEM_1425_sm_SuppFigure1.pdf265KSupplementary Figure S1. Principal Component Analysis (PCA). PCA generated using quantile normalised data from the arrays conducted in this study on the hiPSC lines [L]IMR90C2 and [L]ForeskinC1 and from the hESC lines H9 and MEL1 from Kolle et al., 2009. [A] Separation of hiPSC and hESC samples on component 1 is likely explained by differences in the array version between the published hESC data (V2) and newer hiPSC experiments (V3) and component 2 appears to be driven by TG30/GCTM-2 fractionation. [B] Absolute measure of the percentage variance of each principal component indicating that the data can be explained by the first three components.
STEM_1425_sm_SuppFigure2.pdf216KSupplementary Figure S2. Persistence of P7 cells does not cease with long term in-vitro passaging and presence of OCT4 in P4 cultures. (A): Comparative analysis of Colony Forming Assays (CFA) between late-passage (<50 passages) lentivirally-derived [L]hIPSForeskinC1 and hESC-MEL1 control line. A defined number of P4 (TG30Neg-GCTM-2Neg) cells were cultured post-FACS in 12-well plates, generating an elevated number of hPSC-like colonies only for the lentiviral hiPSC samples. Data collected from three independent CFA (n=3), each assayed in triplicate (mean ± SEM). (B): Immunofluorescence for pluripotency markers. Colonies generated by P4 (TG30Neg-GCTM-2Neg) cells from late-passage lentiviral hiPSC samples, exhibited immunoreactivity to the pluripotency markers OCT4 (red) and NANOG (green). (C): Quantification of OCT4 protein in the P4 (TG30Neg-GCTM-2Neg) population from both hiPSC and hESC lines. P4 exhibits a low level of OCT4 protein and requires the highly sensitive TaqManR Protein Assays for quantification. A defined number of P4 (TG30Neg-GCTM-2Neg) cells was collected by FACS from standard cultures of hiPSC lines (lentiviral [L]hIPS-IMR90C2 and [L]hIPS-ForeskinC1, retroviral [R]hIPS-PDL-D1C6) and hESC control (MEL1), followed by OCT4 protein quantification. Expression levels are shown relative to hESC-MEL1 set to 100%. Data from three independent experiments (n=3), assayed in triplicates, error bars represent SEM. Asterisks highlight statistical significance with respect to the control sample hESC-MEL1. *P<0.05, **P<0.01, ***P<0.001; ns, P<0.05, with a 95% confidence interval.
STEM_1425_sm_SuppTable1.pdf12KSupporting Information

Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.