I run a negative control in qPCR, but I get a Ct value close to 25. I have already changed primers, ddH2O and even SYBR, but the problem still remains..
This could either be an issue of primer-primer interaction (even though you changed the primer sequence), or it could be a primer-probe interaction. I would check the sequences of your probe and determine if you could have complementary sequences.
I use SYBR Green, no TaqMan chemistry. So, I do not have a probe in my reaction. I too thought about primer dimers (checked the melting curves already), but there's more than one gene to show a negative control's Ct value and I think it's not a primer problem - two target genes actually, the housekeeping seems to be ok..!! Pipette problem maybe?? :-p
You may want to specify what your negative control is. Some people use a no-template control (NTC, water instead of cDNA), others use a No-RT Control or a ( A cDNA synthesis reaction made without reverse transcriptase). The interpretation of a CT of 25 for each of these controls is different.
Actually, I have already changed bench (went to another lab to tell the truth) and pipettes and eppendorfs too. And yes, last time I used another PCR machine. The problem still remains...It is strange, isn't it??
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