May 13, 2026
Joint extraction of DNA and RNA from plankton filters using the commercial DNAbsolute kit
- Julie Poulain1,2,3,
- Sophie Oztas1,2
- 1Metabolic Genomics, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. For UMR;
- 2Genoscope, Institut François Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, France, for Genoscope;
- 3Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
Protocol Citation: Julie Poulain, Sophie Oztas 2026. Joint extraction of DNA and RNA from plankton filters using the commercial DNAbsolute kit. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvjkkybgk5/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: May 12, 2026
Last Modified: May 13, 2026
Protocol Integer ID: 316863
Keywords: DNA, RNA, co-extraction, plankton, complex environmental sample, use of the commercial dnabsolute extraction kit, commercial dnabsolute extraction kit, rna from plankton filter, plankton filter, commercial dnabsolute kit this protocol, commercial dnabsolute kit, seawater filtration, joint extraction of dna, rna from complex plankton sample, complex plankton sample, dna, extraction, filter, polycarbonate membrane, rna, joint extraction, idylle company
Funders Acknowledgements:
FRANCE GENOMIQUE
Grant ID: ANR-10-INBS-09
Abstract
This protocol describes the use of the commercial DNAbsolute extraction kit (Idylle Company), with a few modifications to the supplier's protocol, to enable co-extraction of DNA and RNA from complex plankton samples obtained from seawater filtration. Once the water has been filtered through polycarbonate membranes, the filters are flash-frozen in liquid nitrogen and then stored at -80°C until extraction.
Guidelines
Do not incubate the lysate for more than 15 min for RNA purification
Follow the centrifugation speeds and times
Mix gently and use wide-bore tips to avoid shearing the DNA
Volumes may be adapted according to the samples, but the relative proportions of the reagents must always be maintained
It is always advisable to include a negative extraction control.
Materials
Vortex mixer
Sterilized forceps
P1000/200/100 pipettes
Thermomixer for 50 mL tubes at 56°C, allowing shaking at 300 rpm
Incubator or dry block heater at 37°C
Minifuge
Centrifuge for 1.5 mL tubes (10000g) (e.g.: Eppendorf Minispin)
Centrifuge for 50 mL tubes (3000-10000g), equilibrated at 18-21°C - (e.g.: Eppendorf 5810R centrifuge, Rotor, V6.4 for 50 mL tubes)
ZR BashingBead Lysis Tubes (0.1 6 0.5 mm) Ref: S6012-50 Zymoresearch RT
DNAbsolute kit, [ABS-50] DNAbsolute Idylle
- DNAbsolute solution 4°C
- PBS buffer 150 mM RT
- Tris Buffer 25 mM RT
- Lysis buffer 1 RT
- Lysis buffer 2 RT
- PBS buffer 150 mM RT
Proteinase K (20 mg/mL) Ref 19133 Qiagen RT
RNase A (100 mg/mL) Ref 1007 Qiagen RT
- Dilute the solution 1/10 and aliquot in 100 µL volumes RT
Ethanol 100% Ref 12498740 FisherScientific RT
Isopropanol Ref 10657411 FisherScientific RT
NaAc (3 M, pH 5.2) Sodium acetate solution Ref 71196-100ML Sigma RT
DTT, M (Dithiothreitol) 1 M solution Ref: 43816-250mL Sigma +4°C
- Prepare a 0.1 M solution, then prepare 360 µL aliquots -20°C
H2O RNase/DNase-free Ref 10977035 FisherScientific RT
50 mL Falcon tubes
1.5 mL Eppendorf DNA LoBind tubes (DNA)
1.5 mL Ambion DNase/RNase-free tubes (RNA)
Single-use scalpel
Filter tips 1000/200/100 µL
Wide-bore tips 1000/200 µL
Before start
Prepare 70% ethanol
Equilibrate the 50 mL thermoblock to 56°C
Equilibrate the incubator or 1.5 mL thermoblock to 37°C
Equilibrate the DNAbsolute solution at RT ~30 min before use
Equilibrate 100 µL of Tris Buffer at 37°C
Grinding, lysis and Proteinase K digestion
In a 50 mL Falcon tube, preheat one 3600 µL aliquot of Lysis buffer 1 for 5 min at 56°C.
Recover the still-frozen filter using forceps and cut it with a scalpel over the 50 mL tube containing the preheated LB1.
Add 360 µL DTT (0.1 M) = 1/10 Vol (10 mM final) to inhibit RNases.
Pour in the entire contents of one bashing bead tube.
Vortex for 15 sec.
Briefly centrifuge, ramp up and down, 1000g.
Add 360 µL of Proteinase K and mix gently.
Incubate at 56°C / 300 rpm.
After 15 min, collect and transfer 400 µL of the solution into a 1.5 mL RNase-free tube and proceed to the RNA purification step (II).
After 60 min, collect the remaining volume (~3200 µL) using a wide-bore tip, transfer it into a 50 mL tube and proceed to DNA purification (III).
RNA purification
Use a marker to identify the side where the pellet should be located, as it is not always visible.
Centrifuge the tube containing 400 µL of lysate for 3 min at 10000g.
Transfer the supernatant into a new 1.5 mL RNase-free tube.
Add 1 volume of Lysis buffer 2 (400 µL) and vortex for 1 sec.
Add 1 volume of cold isopropanol (400 µL).
Add 1/10 volume of sodium acetate (40 µL).
Mix gently and incubate for 5 min at 4°C.
Centrifuge at 12000g for 15 min.
Carefully remove the supernatant without disturbing the RNA pellet (the pellet is not always visible).
Add 500 µL of 70% ethanol without disturbing the pellet and centrifuge for 5 min at 10000g.
Repeat the 70% ethanol wash a second time.
Carefully remove the supernatant without disturbing the RNA pellet.
Briefly dry the pellet at room temperature. (5-10 min, check dryness)
Resuspend the RNA pellet in 50 µL of RNase-free water.
Quantify using Qubit RNA.
Perform a DNase treatment (e.g., Turbo DNase followed by purification), then store at -80°C.
DNA purification
Use a marker to identify the side where the pellet should be located, as it is not always visible.
Centrifuge the 50 mL tube containing approximately 3200 µL of lysate for 3 min at 10000g.
Using a pipette and a wide-bore tip (1000 µL), transfer the supernatant (~3000 µL) into a new 50 mL tube.
Add 1/100 of the volume (30 µL) of RNase A diluted 1/10 and homogenize by pipetting with a wide-bore tip.
Incubate for 2 min at RT.
Add 1 volume of Lysis buffer 2 (3000 µL) and homogenize.
Add 1 volume of 100% ethanol (3000 µL) and homogenize.
Add 1/2 volume of DNAbsolute reagent (1500 µL) and homogenize.
Use a marker to identify the side where the pellet should be located, as it is not always visible.
Centrifuge for 5 min at 10000g (Accel: 8, Decel 7; option: 16 min at 3000g, but not optimal), then discard the supernatant by pipetting.
Add 200 µL of PBS buffer to the pellet and resuspend it by pipetting using 200 µL wide-bore tips.
Transfer into a 1.5 mL DNA LoBind tube.
Add 1200 µL of 100% ethanol and homogenize using a wide-bore tip.
Centrifuge for 5 min at 10000g.
Discard the supernatant by pipetting.
Perform 2 washes:
Add 600 µL of 70% ethanol
Centrifuge for 1 min, 10000g, at RT
Remove the supernatant
Let the pellet dry for ~10 min at 37°C.
Resuspend with 100 µL of Tris Buffer previously warmed to 37°C.
Quantify using Qubit 1X HS DNA and store at -20°C.
Acknowledgements
This study was supported in part by FRANCE GENOMIQUE (ANR-10-INBS-09)