I want to extract genomic DNA for Illumina sequencing from vibriophages. Screening the literature I came across several methods for phage precipitation. I was wondering
1. which method is the best (PEG precipitation, EtOH precipitation)?
2. is there is any difference in using PEG6000 or PEG8000?
3. is it ok to use a normal DNA extraction kit like DNAeasy (Qiagen) or DNA Wizard purification (Promega)?
I've never done anything with vibriophages specifically, but I did T7 genome extraction for Illumina just a few weeks ago. I didn't precipitate the phages with PEG or anything else and just used a high-titer T7 lysate. Bacterial DNA contamination shouldn't be a big problem with Illumina, since you'd still (presumably) be getting far more phage reads than you'd actually need for assembly. I used standard phenol chloroform extraction (after breaking up the phages with EDTA and SDS), which seemed to work well -- the samples had >300 ng/ul on Nanodrop (the concentration actually looked higher than that on a gel) and passed all of the Illumina quality controls.
Good luck!
thank you Eric! That sounds much easier than anything else I've read until now.
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