Nov 04, 2024

Public workspaceAutomated DNA Extraction from Sediment Samples and Filter Membranes Using Magnetic Beads

DOI
dx.doi.org/10.17504/protocols.io.5jyl8dr8rg2w/v1
  • 1BGI research;
  • 2China National GeneBank;
  • 3MGI Tech
Qianyue Ji
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DOI: dx.doi.org/10.17504/protocols.io.5jyl8dr8rg2w/v1
Protocol Citation: Qianyue Ji, Fangfang Jiang, Xiaohan Wang, Shanshan Liu, Mo Han 2024. Automated DNA Extraction from Sediment Samples and Filter Membranes Using Magnetic Beads. protocols.io https://dx.doi.org/10.17504/protocols.io.5jyl8dr8rg2w/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: Working
We use this protocol and it's working
Created: October 27, 2024
Last Modified: November 04, 2024
Protocol Integer ID: 110976
Abstract
This method presents an optimized protocol for the automated extraction of sediment samples and filter membranes using magnetic beads. DNA was extracted and purified using MGIEasy Stool Microbiome DNA Extraction Kit (940-000122-00, MGI Tech) on a compatible automation system (MGISP-NE384, MGI Tech) .
Materials
Materials
MGIEasy Stool Microbiome DNA Extraction Kit (940-000122-00, MGI Tech)

Supplies:
  • Pipette tips (assorted volumes)
  • Tubes
  • 96-well deep-well plates

Equipment:
  • MGISP-NE384, MGI Tech
  • Micropipettes, various volumes

Preparing Samples
Preparing Samples
Use Amount1 g of each sediment sample or one half of each filter membrane.

Sediment samples were centrifuged in 96-well deep-well plates (3960, Corning) atCentrifigation12.000 rpm for Duration00:05:00 before the extraction, and the supernatant was discarded before extraction.
5m
Filter membranes were cut to small pieces and subjected to extraction directly.
Preparing Reagents
Preparing Reagents
Preparing Reagents
For one reaction, every Amount20 µL Magnetic Beads-T are mixed with Amount300 µL PFB-M, and mix them thoroughly.

Take out 5 U-bottom deep-well plates (MGI, 1000004644), and mark them as 【PFBM + Magnetic beads-T】, 【PW1-M】, 【PW2】, and 【PB】respectively. Add reagents according to Table.
ItemVolume/Well
PFBM + Magnetic beads-T320 μL (PFB-M + Magnetic beads-T mixed liquor) + 240 μL sample
PW1-M400 μL
PW2800 μL
PB120 μL
Input volume of PFB-M, PW1-M, PW2, Magnetic Beads-T, and PB

DNA Extraction
DNA Extraction
Run the Script
Select script provided by the supplier for DNA extraction.
Follow the on-screen instructions to place the consumables, samples, and reagents. Confirm the placement and close the door.
Click 【Run】 to start extraction workflow.
The extracted DNA can be stored at Temperature-20 °C .