NanoString nCounter expression analysis in ESCs and other cell types.

A) Schematic representation of the cell types corresponding to the different conditions used for the NanoString nCounter gene expression analysis, with corresponding developmental stages, culture conditions for ESCs, and expression of known marker genes highlighted. ESCs = Rex1-GFPd2 embryonic stem cells; EGCs SLD21 and SLD22 = two independently generated lines of embryonic germ cells; EpiSCs = epiblast stem cells; EBs = embryoid bodies collected at day 3, 6 and 9 of differentiation (D3, D6, D9); NPCs = neural progenitor cells obtained by direct differentiation of ESCs; MEFs = mouse embryonic fibroblasts; TSC = trophoblast stem cells; XEN = extra-embryonic endoderm stem cells. B) Heat map representing a clustering analysis of the different cell types based on relative NanoString counts (blue = lowly/not-expressed, red = expressed) of known marker genes for which a specific expression pattern between the different conditions is expected. C) Heat map representing a hierarchical clustering analysis and Pearson correlation (blue = low correlation, red = high correlation) of the different cell types basing on global expression values of KRAB-ZFP genes in the different conditions.