Hi there, in my lab we are going to be sequencing 16S with Miseq from stool samples and we are currently in the DNA extraction step.
We are using Qiagen's QiAmp DNA stool mini kit and have performed an additional step of bead beating that gives us twice of the final DNA concentration. The issue is that when we check the integrity we see smear bands.
How important is if we want to see diversity to start with integral DNA?
We think is important, since we don´t have a way to control what DNA is being degraded and we might loose 16S of some bacterias, but we have performed RFLP-PCR and the profiles are very similar and wanted to ask for your experience.
Thanks!
We are using Qiagen's QiAmp DNA stool mini kit and have performed an additional step of bead beating that gives us twice of the final DNA concentration. The issue is that when we check the integrity we see smear bands.
How important is if we want to see diversity to start with integral DNA?
We think is important, since we don´t have a way to control what DNA is being degraded and we might loose 16S of some bacterias, but we have performed RFLP-PCR and the profiles are very similar and wanted to ask for your experience.
Thanks!
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