these samples are cerulein induced pancreatitis model of mice.
I am also getting amplification in NoRT control. Should i increase or decrease the concentration of cDNA for qPCR?
http://www.sciencedirect.com/science/article/pii/S0006291X97967164
Don't know if that answers your question but i found it related.
When you say amplification in NoRT do u mean just a value (as it could just be one odd spike) or a graph with the proper pattern for amplification ? Also if its expressing in the same CT even in the NoRT then there is a problem with the reagents you will have to eliminate them one by one. If the amplification starts above 38 cycles i think it can be considered as negligible and can be eliminated by adjusting the threshold itself.
Have you confirmed the quality of your RNA prior to RT? A bioanalyzer or RNA gel will be the best way to do this.
The pancreas generates the most RNAse of any organ and it is exceedingly difficult to get proper, high-quality RNA from a pancreas without specific modifications to routine protocols.
If NoRT samples have amplification curves, you have DNA in the samples. Even if you have primers in separate exons, they can give nonspecific product on DNA template. So Jordan is right, check the quality of RNA. Are NTC controls without amplification?