Stem Cell Reports (Jul 2016)

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

  • Nathan Salomonis,
  • Phillip J. Dexheimer,
  • Larsson Omberg,
  • Robin Schroll,
  • Stacy Bush,
  • Jeffrey Huo,
  • Lynn Schriml,
  • Shannan Ho Sui,
  • Mehdi Keddache,
  • Christopher Mayhew,
  • Shiva Kumar Shanmukhappa,
  • James Wells,
  • Kenneth Daily,
  • Shane Hubler,
  • Yuliang Wang,
  • Elias Zambidis,
  • Adam Margolin,
  • Winston Hide,
  • Antonis K. Hatzopoulos,
  • Punam Malik,
  • Jose A. Cancelas,
  • Bruce J. Aronow,
  • Carolyn Lutzko

DOI
https://doi.org/10.1016/j.stemcr.2016.05.006
Journal volume & issue
Vol. 7, no. 1
pp. 110 – 125

Abstract

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The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genomic analyses of 58 iPSC from ten laboratories generated using a variety of reprogramming genes, vectors, and cells. Associated global molecular characterization studies identified functionally informative correlations in gene expression, DNA methylation, and/or copy-number variation among key developmental and oncogenic regulators as a result of donor, sex, line stability, reprogramming technology, and cell of origin. Furthermore, X-chromosome inactivation in PSC produced highly correlated differences in teratoma-lineage staining and regulator expression upon differentiation. All experimental results, and raw, processed, and metadata from these analyses, including powerful tools, are interactively accessible from a new online portal at https://www.synapse.org to serve as a reusable resource for the stem cell community.