The establishment of human embryonic stem cell (hESC) lines in 1998 served to set the pace for understanding the molecular biology behind the two hallmark features of stem cells: self renewal and pluripotency. The excitement was generated in the hope that understanding the molecular biology of hESCs would provide a good model for studying early human development, disease and drug discovery and also hold the promise for providing a cure for degenerative human diseases. In spite of the large number of studies, the molecular basis of pluripotency has remained a matter of intrigue ever since the embryonic stem cells (ESCs) were first identified. A considerable percentage of these studies have been transcriptome-based. Interestingly, significant differences are seen not only between mouse and human ESC transcriptomes but also amongst the hESC studies. Nevertheless, a key set of pluripotency genes seem to be common, reinforcing the utility of transcriptome-based approaches in identifying the molecular basis of pluripotency in hESCs.

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