Fig. 6
Quartz-Seq2 classified genes with variable expression within a cell type. a Plotting cells on t-SNE space with the colors representing the intensity of Hoechst 33,342 staining. b Dependence of expression of several genes on the intensity of Hoechst 33,342 staining (G2/M phase, Ccnb1; G1 phase, Ccne1; housekeeping gene, Gnb2l1). Upper panels: ES main population (cluster 1). Lower panels: PrE main population (cluster 4). c Identification of cell cycle-associated genes. Average gene expression of cells in a bin is depicted by color in the heatmap. Bins are arranged in order of Hoechst 33,342 staining intensity. d The number of cell cycle-associated genes identified for each z-threshold. CV values from which the z-score was calculated are as follows. ES cells (z = 4, 1.17; z = 3, 0.91; z = 2, 0.68; z = 1, 0.4). PrE cells (z = 4, 1.1; z = 3, 0.88; z = 2, 0.64; z = 1, 0.39). e Several examples of genes whose expression was variable but not associated with the phase of the cell cycle. f Single-cell qPCR detection of genes with variable expression