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Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

An Erratum to this article was published on 09 January 2012

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We compared bona fide human induced pluripotent stem cells (iPSCs) derived from umbilical cord blood (CB) cells and neonatal keratinocytes (K). As a consequence of both incomplete erasure of tissue-specific methylation and aberrant de novo methylation, CB-iPSCs and K-iPSCs were distinct in genome-wide DNA methylation profiles and differentiation potential. Extended passage of some iPSC clones in culture did not improve their epigenetic resemblance to embryonic stem cells, implying that some human iPSCs retain a residual 'epigenetic memory' of their tissue of origin.

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Figure 1: Derivation and differentiation of iPSCs from neonatal umbilical cord blood cells and foreskin fibroblasts.
Figure 2: Analysis of methylation in CB-iPSCs, K-iPSCs, ESCs and somatic cells.

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Gene Expression Omnibus

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  • 09 January 2012

    In the version of this article initially published, the received date was incorrect. The correct received date is 17 February 2011. The error has been corrected in the HTML and PDF versions of the article.


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G.Q.D. was funded by US National Institutes of Health (NIH) grants DK70055 and DK59279, special funds received by the NIH under the American Recovery and Reinvestment Act (RC2-HL102815). K.K. was supported by NIH (K99HL093212-01), Leukemia and Lymphoma Society (3567-07), and Cooley′s Anemia Foundation. A.P.F. was funded by NIH grants R37CA054358 and P50HG003233.

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K.K., R.Z., K.N. and G.Q.D. conceived the experimental plan. K.K., R.Z., A.D., K.N., J.U., H.H., M.W.L., Y.-H.L. and H.L. performed the experiments. K.K., A.D., P.C. and M.J.A. performed data analysis. A.D., M.J.A. and A.P.F. performed CHARM and guided analysis of methylation. K.K., R.Z., A.D., K.N., J.U., P.C., J.J.C., M.W.L., A.P.F. and G.Q.D. wrote the manuscript.

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Correspondence to Andrew P Feinberg or George Q Daley.

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Competing interests

G.Q.D. is a member of the scientific advisory boards of iPierian, Verastem, Epizyme, Solasia, MPM Capital and Johnson & Johnson.

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Supplementary Tables 1–6, Supplementary Methods and Supplementary Figures 1–15 (PDF 2438 kb)

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Kim, K., Zhao, R., Doi, A. et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 29, 1117–1119 (2011).

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