Is there any possibility that the RNA-seq data do not agree with the qRT-PCR results? I don't have extensive experience in RNA-seq data analysis, thus recently I sent my RNA sample to my collaborator and they did the RNA-seq and analysis work and back to me the processed value. Among the genes, one of the gene should be much lower in one sample vs. the another sample, since I siRNA knocked down the gene specifically in the sample, and my qRT-PCR confirmed it has been knocked down about 70%. But, in the RNA-seq data, the gene levels are almost the same between these two samples! I also checked other genes, that I know will change upon this gene, and their levels look having the right trend in these two samples. Who can explain to me is it possible? They used both Cuffdiff and Gfold methods to analyze.