I'm doing RT-qPCR for a bacterial pure culture under different conditions. My question is that if 16s rRNA primers are used as reference for RT-qPCR, the actual template for the primers in qPCR step is a combination of reverse transcribed 16 rRNA and 16 rDNA gene. If a cell is actively duplicating and assume 1 rRNA copy per cell, in this case the template is 2 copies; while if a cell doesn't replicate, the template is 1 copy. If ths is true, then we can't compare cells from a log phase to a stationary phase. Also 16s rRNA is not a marker for cell number but cell number plus growth state. Am I making sense here?
Thanks a lot!
a question about 16s rRNA as reference in RT-qPCR
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