Table 1.
Reference target primer design and calculation of amplification efficiencies.
Figure 1.
Workflow to identify candidate expressed repeat elements.
Figure 2.
Average expression stability of common reference genes and expressed repeat elements.
Ranking of reference targets depending on their M-values calculated by geNorm. Reference targets with M-values below 0.5 and 0.2 are considered having a ‘high’ and ‘very high’ expression stability, respectively. EREs are indicated in black, commonly used reference mRNAs in grey.
Figure 3.
A: Rank aggregation analysis ordering the reference genes, based on their rank position according to each stability measurement (grey lines), from the most stable (left) to the least stable (right). Mean rank position of each gene is shown in black, as well the model computed by the Monte Carlo algorithm (red line). All EREs, except for sine3, are ranked better than the commonly used reference genes. B: Box plot representation of dispersion of the M-value. Boxes depict first and third quartile and the median is indicated with a line in the middle of the box, outliers are drawn as circles. Reference targets are ranked according to rank aggregation outcome (most stable reference targets on the left).
Figure 4.
Fold change expression of selected genes of interest after normalization with common reference genes (ref. genes) and with ERE reference targets (ERE).
A: Fold change expression of zorba between 0 hpf and 8 hpf. B: Fold change expression of pax6a between adult zebrafish eye and brain tissues. C: Fold change expression of acta2 between slc2a10 MO and scrambled MO injections. D: Fold change expression of acta2 between TGFBRI compound and screening medium treatment.