Do we get any differences in assessment of gene expression using primers from many exons of a genes? In general, it is done using single optimised primer in Realtime PCR. What happens if two optimised primers from different exons of a gene are used for expression analysis?.
if your gene has multiple transcripts, you might get different results with different set of primers.
I think this article can help you
https://www.gene-quantification.de/Derveaux-et-al-The-ongoing-evolution-of-qPCR-Methods-2010.pdf
If your gene of interest has single transcript, then 4 primers will be required (Forward & reverse primer for your gene of interest and Forward & reverse primer for the housekeeping gene).
However, if the target gene has multiple transcripts, you may need more set of primers while the primer set for house keeping gene will remain same.
You may need to optimize all the primers so while designing the primers, please make sure the annealing temperatures for all the primers are within 2-4°C range with each other.
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