Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Cell Stem Cell. 2015 Oct 1;17(4):471-85. doi: 10.1016/j.stem.2015.09.011.


Embryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state. Overall levels of intercellular gene expression heterogeneity are comparable across the three conditions. However, this masks variable expression of pluripotency genes in serum cells and homogeneous expression in 2i and a2i cells. Additionally, genes related to the cell cycle are more variably expressed in the 2i and a2i conditions. Mining of our dataset for correlations in gene expression allowed us to identify additional components of the pluripotency network, including Ptma and Zfp640, illustrating its value as a resource for future discovery.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / genetics
  • Cells, Cultured
  • Glycogen Synthase Kinase 3 / antagonists & inhibitors
  • Glycogen Synthase Kinase 3 / metabolism
  • MAP Kinase Kinase 1 / antagonists & inhibitors
  • MAP Kinase Kinase 1 / metabolism
  • Mice
  • Mouse Embryonic Stem Cells / cytology
  • Mouse Embryonic Stem Cells / physiology*
  • RNA / genetics*
  • RNA / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Single-Cell Analysis
  • Transcriptome*


  • Repressor Proteins
  • Zfp640 protein, mouse
  • RNA
  • Glycogen Synthase Kinase 3
  • MAP Kinase Kinase 1