Digital PCR (ChIP-seq quantitifcation)

[spikey_hedgehog]

Hi

Has anyone used digital PCR to quantify ChIP library concentrations with primers specified in the Illumina qPCR quantification kit, Primer 1.1 and 2.1?

Is it accurate?

Thanks heaps!

[bunce]

Hi, I can't directly answer your question but when we were validating the Quant-studio dPCR platform (using sybr, not probes) we used the p5 and p7 sets to quant some existing MiSeq libraries. The issue for using this routinely for libraries is that you need to land the dPCR in the 'sweet spot' to get an accurate quant. For this reason we are sticking with qPCR rather than quanting via dPCR - it is cheaper and I am not convinced that the enhanced accuracy of dPCR is worth the time/effort/cost (especially considering there can be ~20% variation in cluster density if you run the same library twice).

But to answer your question - yes dPCR using p5/p7 was supremely accurate - the accuracy of both the Quant-studio and Bio-Rad systems was excellent.

Hope these comments are somewhat useful? best, Mike