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

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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

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