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Computational Biology Methods for Characterization of Pluripotent Cells

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Induced Pluripotent Stem (iPS) Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1357))

Abstract

Pluripotent cells are a powerful tool for regenerative medicine and drug discovery. Several techniques have been developed to induce pluripotency, or to extract pluripotent cells from different tissues and biological fluids. However, the characterization of pluripotency requires tedious, expensive, time-consuming, and not always reliable wet-lab experiments; thus, an easy, standard quality-control protocol of pluripotency assessment remains to be established. Here to help comes the use of high-throughput techniques, and in particular, the employment of gene expression microarrays, which has become a complementary technique for cellular characterization. Research has shown that the transcriptomics comparison with an Embryonic Stem Cell (ESC) of reference is a good approach to assess the pluripotency. Under the premise that the best protocol is a computer software source code, here I propose and explain line by line a software protocol coded in R-Bioconductor for pluripotency assessment based on the comparison of transcriptomics data of pluripotent cells with an ESC of reference. I provide advice for experimental design, warning about possible pitfalls, and guides for results interpretation.

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Notes

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Acknowledgments

This work has been supported by the Basque Country Foundation of Science (Ikerbasque).

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Authors and Affiliations

  1. Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014, San Sebastián, Spain

    Marcos J. Araúzo-Bravo

  2. IKERBASQUE, Basque Foundation for Science, Bilbao, Spain

    Marcos J. Araúzo-Bravo

Authors
  1. Marcos J. Araúzo-Bravo
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Correspondence to Marcos J. Araúzo-Bravo .

Editor information

Editors and Affiliations

  1. Ottawa Hospital Research Institute, Ottawa, Ontario, Canada

    Kursad Turksen

  2. Mount Sinai Hospital Samuel Lunenfeld Research Inst, Toronto, Ontario, Canada

    Andras Nagy

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Araúzo-Bravo, M.J. (2015). Computational Biology Methods for Characterization of Pluripotent Cells. In: Turksen, K., Nagy, A. (eds) Induced Pluripotent Stem (iPS) Cells. Methods in Molecular Biology, vol 1357. Humana Press, New York, NY. https://doi.org/10.1007/7651_2015_279

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  • DOI: https://doi.org/10.1007/7651_2015_279

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3054-8

  • Online ISBN: 978-1-4939-3055-5

  • eBook Packages: Springer Protocols

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