Review Article | Published:

Single-cell transcriptional profiling: a window into embryonic cell-type specification

Nature Reviews Molecular Cell Biologyvolume 19pages399412 (2018) | Download Citation


During mammalian embryonic development, a single fertilized egg cell will proliferate and differentiate into all the cell lineages and cell types that eventually form the adult organism. Cell lineage diversification involves repeated cell fate choices that ultimately occur at the level of the individual cell rather than at the cell-population level. Improvements in single-cell technologies are transforming our understanding of mammalian development, not only by overcoming the limitations presented by the extremely low cell numbers of early embryos but also by enabling the study of cell fate specification in greater detail. In this Review, we first discuss recent advances in single-cell transcriptomics and imaging and provide a brief outline of current bioinformatics methods available to analyse the resulting data. We then discuss how these techniques have contributed to our understanding of pre-implantation and early post-implantation development and of in vitro pluripotency. Finally, we overview the current challenges facing single-cell research and highlight the latest advances and potential future avenues.

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B.P.-S. is funded by the Wellcome Trust 4-Year PhD programme in Stem Cell Biology and Medicine and the University of Cambridge, UK. C.G. is funded by the Swedish Research Council. Research in the Göttgens laboratory is supported by programme grants from the Wellcome Trust, CRUK and Bloodwise and by a Wellcome Strategic Award to study cell fate decisions during gastrulation (105031/D/14/Z). The authors also gratefully acknowledge core support funding from the Wellcome Trust to the Wellcome–Medical Research Council Cambridge Stem Cell Institute.

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  1. Wellcome and MRC Cambridge Stem Cell Institute and the Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK

    • Blanca Pijuan-Sala
    • , Carolina Guibentif
    •  & Berthold Göttgens


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B.P.-S. researched data for the article and wrote the article. C.G. contributed substantially to the discussion of the content. B.P.-S., C.G. and B.G. reviewed and edited the manuscript before submission.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Berthold Göttgens.


Fluorescence-activated cell sorting

Flow cytometry method to analyse and sort single cells based on the expression of cell-surface markers.

Microfluidics systems

Automated technologies based on the use of microminiaturized devices for mixing and manipulating low fluid volumes aiming to achieve multiplexing and high-throughput yields.


Embryonic stage composed of inner cell mass cells, a fluid-filled cavity called blastocoel and outer trophectoderm cells.


Group of cells derived from the inner cell mass that will give rise to the embryo proper.

Primitive endoderm

Group of cells derived from the inner cell mass that contribute to extra-embryonic tissues such as the yolk sac.

Unique molecular identifiers

Short sequences that uniquely tag individual RNA molecules.

Dimensionality-reduction approaches

Methods used in high-dimensional datasets, where each gene represents a dimension, to reduce the number of dimensions and elicit the visualization of the data set structure in a two-dimensional or three-dimensional plot.


Embryonic process, following implantation, where epiblast cells become specified into the three germ layers (ectoderm, mesoderm and endoderm).

Inner cell mass

(ICM). Group of cells located inside the blastocyst that will give rise to the primitive endoderm and the epiblast.


Group of cells located on the outer part of the blastocyst that will become the supportive extra-embryonic tissues, such as the placenta.


The cells resulting from the first divisions of the fertilized egg.

Maternal-to-zygotic transition

Process occurring shortly after fertilization, where maternal RNA and proteins are degraded and the zygotic genome is activated and produces RNA and proteins.

Bimodal distribution

In gene expression analyses, a gene being either (a) highly expressed or (b) not or lowly expressed, with small numbers of cells displaying intermediate levels. Cells can thus be divided into two subpopulations based on the expression levels of that particular gene.


Group of inner cell mass cells with heterogeneous expression of epiblast and primitive endoderm markers, where cells expressing more epiblast markers are intermingled with cells expressing more primitive endoderm markers.


Early embryonic stage where the embryo is composed of a symmetric ball of morphologically similar cells.

Primitive streak

Morphological structure at the posterior side of the embryo formed by the accumulation of cells. It is where epiblast cells will ingress to become mesoderm or endoderm.

Mesendodermal progenitor

A cell that can give rise to either mesoderm or endoderm.

Yolk sac

Extra-embryonic tissue that originates from the primitive endoderm.

Boolean algorithm

Qualitative algorithm based on the Boolean (binary) logic, where only two values are accepted. In gene regulatory networks, one value will be active and the other one inactive.

Unimodal distribution

In gene expression analyses, unimodal distribution refers to a gene being mostly expressed at intermediate levels.

X-chromosome reactivation

Process where the inactivated X chromosome in mammalian female cells becomes reactivated.

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