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. Author manuscript; available in PMC: 2018 Jul 8.
Published in final edited form as: Nat Cell Biol. 2018 Jan 8;20(2):127–134. doi: 10.1038/s41556-017-0013-z

Fig. 1. Single-cell RNA-seq of whole mouse E8.25 embryos identifies 20 major cell types.

Fig. 1

A) E8.25 whole mouse embryos were dissociated and processed with the 10X genomics platform to capture single cells and produce libraries for RNA sequencing. A representative image of the sequenced embryos is shown. B) Violin plots indicating the number of UMIs and genes obtained per cell. A boxplot is shown on the inside (center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; n = 19,396 cells). C) t-SNE plot of all the cells that passed quality control (19,396) computed from highly variable genes; the first two dimensions are shown. Cells with similar transcriptional profiles were clustered into 33 different groups, as indicated by the different colours. Each cluster was annotated based on the expression of marker genes into 20 major different cell types. Several cell types are composed of two or more clusters. PSM = presomitic mesoderm.