I used shRNA against a gene to perform knockdown in cancer cell lines but I am not able to see any change in the mRNA expression levels after performing a qPCR. What could be the possible explanation for this problem?
Do you have any positive control indicating that the shRNA you used actually works? Maybe the hairpins are not expressed, or they are not effective against the intended target.
Have you worked on shRNA concentration, transfection methodology, & post-transfection incubation time? I hope you have avoided antibiotics during transfection and preferred pre-serum starvation which increases efficiency.