[Bidfudge]

Feedback on these experiments

I think the original purpose of the Ambion spike-ins was purely as a control to ensure that the lysis buffer was getting to all the wells in the C1 chip and that the RT was working efficiently for each cell (which isn't always the case so the spike-ins have been invaluable to us in that way). I don't think they were intended to be used as a normalization tool, but since they are there, it's tempting to use them. They are simply an artificial, theoretically controlled housekeeping gene in a way.

Yes, the ERCC spike-ins aren't perfect, but I think they do give a lot of information about the variability of the method in general and specifically in each data set. It's much better to have them and not need them than the other way around (which is what happened with us). I think a lot of new data and bioinformatics methods are going to be coming out in the next year or two and having the right tools available in your data now will allow you to access those methods in the future.

Hi Travelk,

Did you published the paper related to the data generated with the C1? I'm facing the same thing, I will have full length RNAseq data from the C1 soon and we used the Spike from Ambion as recommended in the fluidigm's protocol.

Does the spike from Ambion allow you to normalize these datas?

Thanks,