I have to examine the expression profile of some selected genes (transcript) generated from a de novo transcriptome assembly of a non-model plant by Trinity tool in the various samples via qRT-PCR analysis. As you know, the output of Trinity is multiple transcript isoforms of the same gene. Since I want to assay the expression profile in the several samples, which have not been already sequenced and analyzed, I have no idea which isoform will be differentially expressed during qRT-PCR analysis. So, I am not sure which isoform should be considered for primer designing. I also thought about designing primer pairs from similar regions of all isoforms, but I still cannot make decision what I should do. Could you please help me on this issue?
Your hep would be highly appreciated.