Cellular and Molecular Life Sciences

, Volume 71, Issue 14, pp 2707–2715 | Cite as

Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos



Cellular heterogeneity within a cell population is a common phenomenon in multicellular organisms, tissues, cultured cells, and even FACS-sorted subpopulations. Important information may be masked if the cells are studied as a mass. Transcriptome profiling is a parameter that has been intensively studied, and relatively easier to address than protein composition. To understand the basis and importance of heterogeneity and stochastic aspects of the cell function and its mechanisms, it is essential to examine transcriptomes of a panel of single cells. High-throughput technologies, starting from microarrays and now RNA-seq, provide a full view of the expression of transcriptomes but are limited by the amount of RNA for analysis. Recently, several new approaches for amplification and sequencing the transcriptome of single cells or a limited low number of cells have been developed and applied. In this review, we summarize these major strategies, such as PCR-based methods, IVT-based methods, phi29-DNA polymerase-based methods, and several other methods, including their principles, characteristics, advantages, and limitations, with representative applications in cancer stem cells, early development, and embryonic stem cells. The prospects for development of future technology and application of transcriptome analysis in a single cell are also discussed.


Single cells Transcriptome RNA-seq Cancer stem cells Embryonic stem cells 


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Copyright information

© Springer Basel 2014

Authors and Affiliations

  1. 1.State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life ScienceNankai UniversityTianjinChina
  2. 2.Department of Genetics, Yale School of MedicineYale UniversityNew HavenUSA

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