Jump to main content
Jump to site search

Issue 8-9, 2009
Previous Article Next Article

Single-celltranscript analysis of human embryonic stem cells

Author affiliations


We demonstrate the qualitative and quantitative power of single-celltranscript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC’s). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency. Using single-cell analysis of H9 hESC’s differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers. Our single-cell profiles reveal mixed populations of cell types, with both transcriptional and temporal heterogeneity marking differentiation under all conditions. Interestingly, we also observe extensive and prolonged co-expression of markers regulating both pluripotency and lineage differentiation in all culture conditions, and we find that pluripotency marker transcripts remain detectable in the majority of cells for many days. Finally, we show that cells derived from undifferentiated hESC colonies display consistent gene expression profiles characterized by three cohorts of transcripts: uniform, absent and sporadically detected messages, and that a striking correlation exists between genes’ membership in these cohorts and their hESC promoter chromatin state, with bivalent promoters dominating the sporadic transcripts.

Graphical abstract: Single-celltranscript analysis of human embryonic stem cells

Back to tab navigation

Supplementary files

Publication details

The article was received on 27 Apr 2009, accepted on 02 Jul 2009 and first published on 30 Jul 2009

Article type: Paper
DOI: 10.1039/B908276J
Citation: Integr. Biol., 2009,1, 540-551

Search articles by author