Figure 8
Comparison of E3.25-E4.5 stage inner cells (Ohnishi et al.3) with all existing ESC Affymetrix Mouse Genome 430 2.0 Array transcriptomics profiles. (A) PCA. Green circles and dodecahedra mark E3.25 LNCs and HNCs, respectively. Cyan circles and dodecahedra mark E3.5 and E4.5 PE, respectively. Blue circles and dodecahedra mark E3.5 and E4.5 EPI, respectively. Orange circles mark ESCs. (B) Heat map of the 1 - Spearman correlation distances of the top-closest ESC to the different pre-implantation developmental stages. (C) Histogram of the distribution of the distance between the transcriptomics profiles of each of the E3.25–E4.5 single cells of Ohnishi et al.3 and each one of all of the ESC Affymetrix Mouse Genome 430 2.0 Array transcriptomics profiles. The shadowed rectangle marks the range of distances between the top-closest ESC and E3.25 HNC. (D) Pairwise scatter plots of ESC 2i + LIF vs E3.25-HNC. The black lines are the boundaries of the 2-fold changes in gene expression levels between the paired samples. Transcripts up-regulated in ordinate samples compared with abscissa samples, are shown with red dots; those down-regulated, with green. The positions of some markers are shown as orange dots. The colour bar indicates the scattering density. Darker blue colour corresponds to higher scattering density. The expression levels are log2 scaled. ρ is the Pearson’s correlation coefficient. The E3.25 HNC-h-DEGs are over-imposed as yellow dots.
