I did taqman assays for the cDNAs from mouse skin biopsies. There were six different groups containing 5 animals each.
We isolated RNA from all the skin biopsies individually and synthesised the cDNA after DNA clearance (3µg RNA used).
When I analysed the data, for one group alone in all the 5 mice, the Ct values of both HPRT (internal control) and target gene were very high in the range of 35-40. For all the other groups the Ct values of HPRT was around 25-30 and the target gene around 30-35.
The RNA concentrations were good. In agarose gel, I could see the two RNA subunit bands.
What is the problem here? How can I lower the Ct values in this particular group?
Thanks in advance.