Valproic acid treatment changes expression of only a small proportion of genes in embryonic stem cells. Embryonic stem (ES) cells (CCE/R) were treated for 8 h with 1 mM valproic acid (VPA) and the NIA15K cDNA microarray was used to compare gene expression in control and treated cells. The use of three biological replicates allowed statistical testing (t-tests) to classify genes by the level of significance (P- value) of their expression change. (A) Genes for which the change in transcript level (up or down) had a P- value after FDR correction, equal to or less than 0.1, and a mean change of at least 1.5-fold, were classed as up- or down-regulated, as indicated. The histogram shows the numbers of genes where the significant fold change is 1.5- to 2.0-fold (light grey) or >2.0-fold (dark grey). (B) Heat map showing gene expression change in three replicate experiments along with a list of representative genes showing different levels of change. (C) To validate microarray results, representative transcripts were quantified by real time-quantitative (RT-q)PCR in untreated and VPA-treated cells. Error bars represent the standard error of the mean of independent experiments (n = 3). To assess significance of a change, two-tailed unpaired t-tests were performed using the GraphPad software; *P <0.05.