Aug 30, 2025
eDNA Extraction Protocol from Water Samples Using GFF Filters and Bento Lab
- Vid Švara1
- 1FH Kärnten gGmbH
Protocol Citation: Vid Švara 2025. eDNA Extraction Protocol from Water Samples Using GFF Filters and Bento Lab. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6zd4dgqe/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: August 29, 2025
Last Modified: August 30, 2025
Protocol Integer ID: 225824
Keywords: dna exctraction from filter, extraction protocol from water sample, dna exctraction, gff filter, using gff filter, water sample, extraction protocol, filter, dna
Funders Acknowledgements:
ÖAW
Grant ID: DI-2023-035
Abstract
A protocol aiming at DNA exctraction from filters using spin columns.
Materials
Bento Lab (centrifuge, heat block, PCR thermocycler, blue light illuminator)
Microcentrifuge tubes (1.5 mL, sterile)
Pipettes (P200, P1000) with sterile filtered tips
Vortex mixer (optional but recommended)
Ethanol 96–100% (molecular biologygrade)
Qiagen DNeasy Blood and Tissue Kit
GFF filters in 5 mL tubes with 1 mL ATL buffer (Qiagen)
Proteinase K (included in DNeasy Blood and Tissue Kits)
Nuclease-free water
PCR tubes and reagents
Primers 10 µM
Master mix Qiagen Multiplex PCR Plus Kit
Troubleshooting
Sample Lysis
Add 20 µL of Proteinase K to each 5 mL tube containing the filter and ATL buffer.
Vortex briefly or manually shake to mix.
Incubate the tubes in the Bento Lab heat block at 56 °C for 1–3 hours, or overnight for better yield. Ensure
filters are fully submerged.
After the incubation, transfer 400 µL of the lysate (avoiding large filter
fragments) into a new 1.5 mL tube.
DNA binding
Add 400 µL volume (1:1) of AL buffer to the lysate and mix thoroughly.
Add 400 µL volume of 96–100% ethanol and mix again (vortex or pipette up and down).
Apply 600 µL of the mixture to a Qiagen spin column in steps; centrifuge at 6,000–8,000 rpm for 1 min in Bento Lab centrifuge.
Discard flow-through each time and repeat until all of the lysate from the 1,5 mL tube
is centrifuged through the column.
Perform the wash steps according to the original protocol
DNA Elution
Place spin column in a new 1.5 mL Eppendorf tube.
Add 80 µL of Buffer AE or nuclease-free water.
Incubate at room temperature for 1 min, centrifuge 1 min to elute DNA.
An Inhibitor removal can be performed on each sample or the samples can be stored at -20 °C until further analysis.