Cell
Volume 144, Issue 3, 4 February 2011, Pages 439-452
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Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

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Summary

The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line-specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Toward this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines.

Highlights

► Genome-wide maps of DNA methylation and gene expression for 32 ES and iPS cell lines ► Some but not all iPS cell lines fall within the spectrum of observed ES cell variation ► Epigenetic and transcriptional defects can interfere with in vitro differentiation ► High-throughput assay quantifies cell-line-specific differentiation propensities

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These authors contributed equally to this work