Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation

Ali Fathi, Mohammad Pakzad, Adele Taei, Thore C. Brink, Leila Pirhaji, Guifré Ruiz, Mohammad Sharif Tabe Bordbar, Hamid Gourabi, James Adjaye, Hossein Baharvand*, Ghasem Hosseini Salekdeh

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

51 Citations (Scopus)


Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal and pluripotency. We employed a 2-DE-based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and different stages of spontaneous differentiation (days 3, 6, 12, and 20) by embryoid body formation. Out of 945 proteins reproducibly detected on gels, the expression of 96 spots changed during differentiation. Using MS, 87 ESC-associated proteins were identified including several proteins involved in cell proliferation, cell apoptosis, transcription, translation, mRNA processing, and protein folding. Transcriptional changes accompanying differentiation of Royan H5 were also analyzed using microarrays. We developed a comprehensive data set that shows the use of human ESC lines in vitro to mimic gastrulation and organogenesis. Our results showed that proteomics and transcriptomics data are complementary rather than duplicative. Although regulation of many genes during differentiation were observed only at transcript level, modulation of several proteins was revealed only by proteome analysis.

Original languageEnglish
Pages (from-to)4859-4870
Number of pages12
Issue number21
Publication statusPublished - 1 Nov 2009
Externally publishedYes


  • Cell biology
  • Differentiation
  • Embryonic stem cells
  • Human
  • Microarray


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