This is absolutely possible. There is a protocol in the Bio-Rad ddPCR Application Guide (pages 101-103) for disrupting the emulsion using chloroform and centrifugation to bring everything back into the aqueous phase and remove the oil so the PCR products can be run on a gel.

You can find a copy of the guide here: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6407.pdf

Hi,

I am curious why you think you have multiple products?

Using ddPCR, you would expect to see extra clouds or 'tell tale clouds' which hint towards an extra/different amplicon. This amplicon could be a sequence variant, something aspecific or a splice-variant (with cDNA). You can find information in the same guide as mentioned above https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6407.pdf pages 111 - 112.

To put the fragments on a gel, you can indeed use the protocol mentioned by Jacob L. H. Mclaughlin . But I would argue that the ddPCR plots themselves already might give you the info you are looking for!

Thanks so much for the responses! This is super helpful, i’ll try that emulsion disruption protocol out and see how it looks Jacob L. H. Mclaughlin

@Caroline weydert when you say “tell tale clouds” are you referring to regions on the ddPCR amplification plot where there are a high number of positive droplets? In our lab we always refer to that as the “rain”, not sure if that’s what you’re referring to. Thanks again so much for the discussion! Much appreciated

Hi,

With a 'tell tale cloud' I mean an extra population on the 2D plot (see the attached picture from the applications guide https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6407.pdf). It can be anywhere on the plot. Typically aspecific amplification gives an extra population above the baseline. I hope this helps!