Fig. 1
Identification of a stem cell-state-specific gene expression pattern. a Heat-map of expression of 24 genes (Ct values) for freshly isolated single HSCs and MPPs. Expression values combined and clustered for HSC, MPP1, MPP2, and MPP3 cells (Number of single cells for HSC n = 28, MPP1 n = 28, MPP2 n = 31, MPP3 n = 37, total n = 124). Colored squares indicate the population of origin for each single cell (red, HSC; green, MPP1; blue, MPP2; turquoise, MPP3). b Gene expression values of freshly isolated single HSCs and MPPs after principal component analysis (PCA). Individual cells are projected on the first two principal components PC1 and PC2. Colored points belong to the indicated populations (red, HSC; green, MPP1; blue, MPP2; turquoise, MPP3). Assuming Gaussian distributions, ellipses show the 75% regions of highest density. c PC1 and PC2 coefficients for all single cells are shown on boxplots. Center lines indicate mean. Box limits indicate twenty-fifth percentile and seventy-fifth percentile. Whiskers indicate extreme data points excluding outliers. Crosses indicate outliers. d Eigen values of the 24 principal components, indicating the contribution level of principal components PC1 and PC2 selected for the two-dimensional analysis. e Heat-map of the coefficients of PC1 and PC2 vectors, corresponding to the weights attributed to each gene by each principal component. f Violin plots showing the distribution of gene expression levels for 12 selected genes between HSC, MPP1, MPP2 and MPP3. Genes selected based on ANOVA on HSCs and MPPs (p ≤ 0.01). Squares indicate the mean. Vertical lines indicate the standard deviation. Gray areas indicate Kernel probability density. Horizontal lines indicate significance in t-test pairwise comparisons with p ≤ 0.01. See also Supplementary Fig. 1
