Additional file 9.

MA plots illustrating differential gene expression from both Illumina and SOLiD data. For the longest isoform of each locus from the Illumina+ assembly, the expression fold change (log2 scale) relative to the control (0 h) is plotted against its log average abundance (MA plot). Statistically significant up- or down-regulation (adjusted P-value < 0.001 and log2 fold change > 0.7 or < -0.7 (red lines)) is indicated in yellow and blue, respectively. Genes chosen for qRT-PCR validation (Figure 5) are labeled. (a-e) MA plots show a comparison of Illumina transcriptome sequencing (RNAseq) data from 0.5 to 1 h samples (a), 2 to 3 h samples (b), 4 to 8 h samples (c), 10 to 18 h samples (d) and 24 to 72 h (e) relative to controls. (f, g) SOLiD reads from control or regeneration samples were aligned to the genomic supercontigs with Bioscope. MA plots show a comparison of SOLiD RNAseq data from 1 h sample (f) and 6 h sample (g) relative to controls.

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Sandmann et al. Genome Biology 2011 12:R76   doi:10.1186/gb-2011-12-8-r76