input DNA for Illumina´s Nextera XT sample prep kit

[alpinedna]

Hi All-

I am generating PCR product of DNA sampled from water (environmental DNA). The amplicons range in size from 650-790 bp. This is the input DNA I would like to use for the Nextera XT sample prep kit from Illumina. I have asked their tech support with out much help on this topic...

If I have a nice clean and tight PCR band on a gel, is there any reason why one can not use exo and sap to "clean" the PCRs before diluting the DNA to 1 ng/uL?

I have over 600 PCRs and doing gel extraction or even a magnetic bead clean up is too much time and money.

Thanks!!
alpinedna

[SarahNGS]

PCR clean-up for sequencing

Hi All-

I am generating PCR product of DNA sampled from water (environmental DNA). The amplicons range in size from 650-790 bp. This is the input DNA I would like to use for the Nextera XT sample prep kit from Illumina. I have asked their tech support with out much help on this topic...

If I have a nice clean and tight PCR band on a gel, is there any reason why one can not use exo and sap to "clean" the PCRs before diluting the DNA to 1 ng/uL?

I have over 600 PCRs and doing gel extraction or even a magnetic bead clean up is too much time and money.

Thanks!!
alpinedna

Alpineda,
Given how much money you are about to spend sequencing these samples, and the potential precious nature of them, I would not risk it. Do the magnetic bead clean-up! If you do it in a 96-well plate it shouldn't take too much time at all. A simple clean-up with 0.6x bead volume would suffice.