Figure 3

RT-qPCR validation experiments. GeNorm and mean Cq values from the RT-qPCR validation experiments carried out on samples from Mouse, Arabidopsis, Human, Cattle, and Pig. Novel reference gene candidates (blue) identified with the RefGenes tool were compared to commonly used reference genes (yellow). The first section shows the results for tissues that were abundantly represented in Genevestigator and for which novel reference genes were proposed by RefGenes. In this case, the candidates proposed by RefGenes generally performed better according to GeNorm than commonly used reference genes. The second section shows RT-qPCR results for human lymphoblastoid cell lines (LCLs). Novel reference genes were identified from a a set of human LCLs and related tissues, because there were too few arrays available for this specific tissue type alone. The third section shows results in cattle and pig liver. Because at the time of writing this article no cattle and pig expression data were available in Genevestigator, novel reference gene candidates were identified with RefGenes from mouse liver samples and extrapolated to orthologs from cattle and pig. The GeNorm values indicated ("GeNorm (Avg M)") represent the average of the expression stability values M of the remaining genes after removal of the least stable one (see full results in Additional file 6). For all experiments, the average GeNorm and Cp values for the top 3 genes, the novel genes identified from RefGenes, and the commonly used reference genes are shown. In all cases, the average Cp values of candidates found by RefGenes were lower than those of commonly used reference genes.