Figure 3

Time-resolved transcriptome analysis identifies an Hdac1-regulated gene expression programme that is sustained throughout neurogenesis. Cluster3.0 analysis of the transcriptomes of Hdac1ATG1 and Standard Control (StCo) morphant embryos at 12, 18 and 27 hpf. Up-regulated probes are indicated in red; down-regulated probes are indicated in green; unchanged probes are indicated in black. The threshold for statistically significant differential expression was set at p < 10^-5 and an additional fold-change minimum of 1.5 was also imposed. All probes on the array are grouped based on their expression changes across the three time points. Large numbers of gene changes were identified as being misregulated at individual time points, however 803 probes were found to be misregulated at all three time points. Only 199 probes were consistently up-regulated (red, arrow) and 335 probes were found to be down-regulated (green, arrow). Probes that exhibited sustained fold-changes in expression >2-fold across all three time points are listed and annotated in Additional file 3, of which those that also exhibited altered expression in hdac1 mutant embryos are listed in Figure 4.