Additional file 1.
Identification of Hdac1-regulated genes using morpholino knock down of hdac1. (A) Histograms of gene expression in Hdac1ATG1 and Hdac1SPL1 morphant embryos, measured against the Standard Control morphant common reference. Using a p-value of <10-5 as cut-off for statistical significance, 7117/43427 microarray probes were identified that exhibited altered expression in Hdac1ATG1 morphants, of which 2557 probes exhibited >2-fold increased or decreased transcript abundance. By comparison, 16638/43427 probes were found to exhibit altered expression in Hdac1SPL1 morphants, of which 4391 probes exhibited >2-fold increased or decreased transcript abundance. Interestingly, however, whereas the Hdac1SPL1 morphant transcriptome exhibited many more differentially regulated genes overall than the Hdac1ATG1 transcriptome, 122 genes exhibited an 8-fold or greater change in expression as a result of the Hdac1ATG1 morpholino, as compared to 56 genes in the Hdac1SPL1 morphants. (B) Array cluster analysis of the transcriptomes of hdac1 mutant, Hdac1ATG1 and Hdac1SPL1 morphant embryos at 27 hpf. Cluster Tree depicts the degrees of similarity between datasets for all probes on each of individual arrays used and was carried using Cluster 3.0 analysis programme. Specific array IDs and the Hdac1 sample used are indicated. Remarkably, two of the hdac1 mutant technical duplicate datasets (10020_1 and 10020_3) cluster more closely with two of the Hdac1ATG1 biological duplicates (10085_1 and 10011_1) than they cluster with their dye-swap duplicates (10020_2 and 1002_4). The Hdac1SPL1 morphant (Splice) datasets cluster less closely with hdac1 mutant data, mostly clustering with Hdac1 Control morphant (HCo) data.
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Harrison et al. BMC Genomics 2011 12:24 doi:10.1186/1471-2164-12-24