Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines

Ying Liu, Soojung Shin, Xianmin Zeng, Ming Zhan, Rodolfo Gonzalez, Franz Josef Mueller, Catherine M. Schwartz, Haipeng Xue, Huai Li, Shawn C. Baker, Eugene Chudin, David L. Barker, Timothy K. McDaniel, Steffen Oeser, Jeanne F. Loring, Mark P. Mattson, Mahendra S. Rao

Research output: Contribution to journalArticle

Abstract

Background: In order to compare the gene expression profiles of human embryonic stem cell (hESC) lines and their differentiated progeny and to monitor feeder contaminations, we have examined gene expression in seven hESC lines and human fibroblast feeder cells using Illumina® bead arrays that contain probes for 24,131 transcript probes. Results: A total of 48 different samples (including duplicates) grown in multiple laboratories under different conditions were analyzed and pairwise comparisons were performed in all groups. Hierarchical clustering showed that blinded duplicates were correctly identified as the closest related samples. hESC lines clustered together irrespective of the laboratory in which they were maintained. hESCs could be readily distinguished from embryoid bodies (EB) differentiated from them and the karyotypically abnormal hESC line BG01V. The embryonal carcinoma (EC) line NTera2 is a useful model for evaluating characteristics of hESCs. Expression of subsets of individual genes was validated by comparing with published databases, MPSS (Massively Parallel Signature Sequencing) libraries, and parallel analysis by microarray and RT-PCR. Conclusion: we show that Illumina's bead array platform is a reliable, reproducible and robust method for developing base global profiles of cells and identifying similarities and differences in large number of samples.

Original languageEnglish (US)
Article number20
JournalBMC Developmental Biology
Volume6
DOIs
StatePublished - May 3 2006
Externally publishedYes

ASJC Scopus subject areas

  • Medicine(all)

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    Liu, Y., Shin, S., Zeng, X., Zhan, M., Gonzalez, R., Mueller, F. J., Schwartz, C. M., Xue, H., Li, H., Baker, S. C., Chudin, E., Barker, D. L., McDaniel, T. K., Oeser, S., Loring, J. F., Mattson, M. P., & Rao, M. S. (2006). Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines. BMC Developmental Biology, 6, [20]. https://doi.org/10.1186/1471-213X-6-20