Hello everyone,
I have filtered some samples of lake water through PES filters (pore size 0.22 um, filter diameter 73 mm). From these filters I will need to extract DNA for metagenomic analysis.
I searched online and found that many kits (e.g. DNeasy) are actually not really good to work with PES filters. Is there a better way to extract DNA from PES?
Best regards and thank you in advance!
Nataliya Teteneva
Hi there Nataliya,
a few colleagues, here in Australia, are using the DNeasy Blood and Tissue kit after using the mini glass beads to pulverize the filter. if you pulverize the filter (without trying to separate filter from DNA), the results are actually pretty good. However, it is true that we are mostly using the DNA for metabarcoding analysis (using short reads), which means I cannot guarantee you will obtain very long DNA sequences after pulverization..
Hope this helps!
you can probably just put your filter into 50ml falcon add 10 mi of pbs or water and vortex it for some time to remove everything from the filter... Francesco method should work as you as you do not have 'naked " DNA on the filter,
so you dont shred your DNA... and you probably use Illumina anyway so no worries about DNA size.
Either aseptically cut your filter into smaller pieces or roll it so the filter faces the inside of a Falcon tube (15 or 50mL with the size of your filter). The best solution would be to add sterile beating beads (zirconium beads or something similar - BioSpec or OPS Diagnostics can help there) and some sort of extraction buffer. Bead-beat on a dedicated device or vortex adapter (used to be available from MoBio). I would use a kit specifically designed for environmental samples for DNA purification (lake water can contain humic acids that may interfere with your downstream DNA processing).
Edit: The Qiagen DNEasy PowerWater Kit might be exactly what you want to use.
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