I have a question concerning RNA_Seq and PCR analysis results. We performed an experiment in which we interfered with the expression of one gene of interest in order to change the effect on the functionally correlated genes. We performed the experiment using 2 replicates: 2 for treatment (interference) and 2 for control (not interfered gene). Through the PCR we verified that the gene was interfered properly and hence not expressed and this resulted with respect to both controls. Then we performed the RNA_Seq analysis on the full transcriptome but surprisingly there is not a statistically significant difference between the expression of the gene of interest between the treatment and the control although the cell lines were not changed between PCR and RNA_Seq, i.e. the samples were the same. We expected a confirmation of the PCR experiment.
Can anyone help me to explain such a strange behaviour between the two experiments?