Fig. 1

Global analysis of the valproic acid (VPA)-induced differentially expressed genes in human embryonic stem cells (hESCs) and human induced pluripotent stems cells (hiPSCs). a hESCs and hiPSCs were differentiated towards all three germ layers and their derivatives for 14 days in the presence and absence of VPA. Samples from three biological replicates were collected on day 0 and day 14 for the microarray studies. b CellNet analysis of the.CEL files shows the ESC classification score, which represents the pluripotency status of hESCs and hiPSCs on day 0 and differentiated cells at day 14. c Two-dimensional principle component analysis (2D-PCA) of differentially expressed genes (hESCs or hiPSCs at day 0 vs 14 days of differentiation, absolute fold change ≥ 2, p < 0.05; 14-day differentiated hESCs or hiPSCs in the presence and absence of VPA, with absolute fold change ≥ 2, p < 0.05). The PCA illustrates a significant variance in the gene expression level in PC1 from day 0 to day 14 in the absence of VPA, whereas PC2 represents variance in the expression level of genes induced by VPA. d “Developmental” probe sets are defined as differentially expressed probe sets on day 14 of differentiation, compared with undifferentiated H9 hESCs, values are for foreskin hiPSCs and the IMR90 hiPSCs on day 0 (absolute fold change ≥ 2, FDR corrected p value < 0.05). e Venn diagram of the developmental PS, showing up- and downregulated genes. f, g Numbers and Venn diagrams of the differentially expressed probe sets (absolute fold change ≥ 2, FDR-corrected p value < 0.05) after exposure to VPA for 14 days, compared with 14-day differentiated H9 hESCs, foreskin hiPSCs and IMR90 hiPSCs. h Hierarchical cluster analysis of significantly deregulated transcripts (absolute fold change ≥ 2, p < 0.05) in 14-day untreated versus VPA-treated cells (Partek Genomics Suite). The results are represented as a heatmap, with gene expression level of the probe set given by blue: low; and red: high