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. 2017 Nov 3;8:1297. doi: 10.1038/s41467-017-01415-5

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — Single-cell RNAseq reveals loss of heterogeneity in the E4.0 mid ICM compared to early E3.5 ICM. Principal component analysis (PCA) based on scRNAseq data from trophectoderm (E3.5), early (E3.5, 10–25 cells per ICM) and mid (E4.0, 20–40 cells per ICM). ICM cells on the 1000 most variable genes (a) and on published pluripotency and differentiation candidate genes (n = 23, list in d) (b). Different stages are designed by different colours. n = 14, 23 and 5 cells, respectively, for E3.5 ICM, E4.0 ICM and E3.5 TE (details of each single cell is listed in Supplementary Data 1). c Hierarchical clustering (top) and Pearson distance (bottom) of pluripotency and lineage genes (listed in d) expression variation in E3.5 and E4.0 single cells, based on Pearson’s correlation. Cells were clustered by lineage (TE, PrE and Epi), then by stage. n = 42 single-cell samples. d Level of expression of the 23 candidate genes involved in pluripotency and lineage differentiation in the 42 single-cell samples and used to classify cells according to their lineage are shown. Cells were ordered according to the hierarchical clustering in c. TE trophectoderm, PrE primitive endoderm, ICM inner cell mass, Epi epiblast