Jun 11, 2025

Public workspaceDNA extraction from fish tissue using the Wizard® SV 96 Genomic DNA Purification System (Promega)

DOI
https://dx.doi.org/10.17504/protocols.io.14egnydm6v5d/v1
DNA extraction from fish tissue using the Wizard® SV 96 Genomic DNA Purification System (Promega)
  • Hervé Rogissart1,
  • Cecile Chardon1,
  • Allan Raffard1
  • 1UMR CARRTEL (USMB-INRAE)
Hervé Rogissart
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DOI: https://dx.doi.org/10.17504/protocols.io.14egnydm6v5d/v1
Protocol Citation: Hervé Rogissart, Cecile Chardon, Allan Raffard 2025. DNA extraction from fish tissue using the Wizard® SV 96 Genomic DNA Purification System (Promega). protocols.io https://dx.doi.org/10.17504/protocols.io.14egnydm6v5d/v1
Manuscript citation:
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: June 06, 2025
Last Modified: March 09, 2026
Protocol Integer ID: 219727
Keywords: DNA extraction, Fish, DNA Purification, dna extraction from fish tissue, dna extraction procedure, genomic dna from fish tissue, dna extraction, summary sheet of the dna extraction procedure, genomic dna purification system, extracting genomic dna, wizard genomic dna purification kit, fish tissue, dna, purification, promega, genomic, fin tissue, procedure
Funders Acknowledgements:
Pôle ECLA (OFB, INRAE, USMB)
Grant ID: ACCLIMATE
Abstract
This protocol describes a method for extracting genomic DNA from fish tissue (e.g., fin tissue) using the Wizard Genomic DNA Purification kit (Promega), adapted from the manufacturers’ recommendations. A summary sheet of the DNA extraction procedure is included to support its practical implementation in the laboratory.
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‱Hervé Rogissart
Materials
  • Samples
- Fish tissue preserved in ethanol (final concentration > 90 % of ethanol) or at -20 °C
- Weight required = 10-15 mg

  • Reagents
To clean the workspace
- DNA/RNA-ExitusPlus
- Ethanol (70 %)

For prepare sample:
- Ethanol 96 - 100 %
- Water

For DNA extraction
- DNA extraction kit: Wizard Genomic DNA Purification kit
- Ethanol 96 - 100 %, molecular grade to prepare wash buffer
- Nuclease-Free Water

  • Materials (excluding solutions preparation)
- Vac-Man® 96 Vacuum Manifold
- Vacuum trap for waste collection - Vacuum pump with tubing
- 96-well deep well plate
- Adhesive plate sealers - Bunsen burner
- Chisel and lab pincer
- Balance
- Specific DNA-work station (sterile area equipped with air filtration)
- Horizontal vortexer with microtube holder
- Vortexer
- Stove (to have 55 °C)
- Pipettes: 100-1000 μL; 10-100 μL or Multichannel pipettors: 10-1,000 µL - 2 trash cans: 1 for liquid and 1 for solid

  • Consumables
- Tips with filter:
> 1000 μL
> 100 μL
- Gloves

Protocol materials
ReagentQubit™ dsDNA BR Assay KitThermo Fisher ScientificCatalog #Q32853
ReagentWizard® SV 96 Genomic DNA Purification SystemPromegaCatalog #A2370
ReagentProteinase K 20 mg/ml SOLUTION (STABILISEE)eurobioCatalog #GEXPRK01-I5
Troubleshooting
Safety warnings
Safety informations of all buffers are availabe at: Safety Data Sheets
Before start
Wear gloves througout the extraction process.
  1. Preheat dry bath or stove to Temperature55 °C
  2. Clean the workspace with DNA-ExitusPlus followed by Concentration70 % volume ethanol
  3. Unpack ReagentWizard® SV 96 Genomic DNA Purification SystemPromegaCatalog #A2370
  4. Check/Prepare solutions

-> Proteinase K Solution
  • Ready-to-use solution: ReagentProteinase K 20 mg/ml SOLUTION (STABILISEE)eurobioCatalog #GEXPRK01-I5
  • Store at Temperature4 °C

-> Column Wash Solution (CWA):
  • Add Concentration95 % volume ethanol to the CWA bottle as directed on the bottle label
  • Store at TemperatureRoom temperature

Prepare sample:
  • Before start
- Organize the samples based on the plate map
- Decontaminate cutting tools: clean with DNA ExitusPlus, rinse with water and cover with ethanol
- Sterilize cutting tools using bunsen burner
  • Cut approximatively 10–15 mg of tissue
  • Place tissue in dedicated well of 96-Well Deep Well Plate
Note
- Decontaminate or replace cutting tools for each sample to prevent cross-contamination
- Cutting the tissue into small pieces may enable more efficient lysis
- Store at Temperature+4 °C for quick use (< Duration08:00:00 ) or at Temperature-20 °C for further use (>Duration08:00:00 )

Lyse sample:
  • Prepare the lysis mixture containing the following per sample
Digestion Solution Master Mix
200 µL Nuclei Lysis Solution
50 µL 0.5M EDTA (pH 8.0)
20 µL proteinase K, 20 mg/ml
5 µL RNase A Solution, 4 mg/ml
Lysis mixture composition
Note
- Homogenize Digestion Solution Master Mix
- When preparing the mix for multiple samples, include an extra volume equivalent to 1 to 1.5 additional samples per every 8 samples
  • Add Amount275 mL lysis mixture to each sample in the 96-well deep well plate
  • Incubate at Temperature55 °C for at least Duration18:00:00 in a stove

Note
- Make sure the incubator is preheated to 55°C otherwise the lysis time must be increased
- Cover the plate with an adhesive plate sealer
- To prevent condensation or liquid accumulation on the sealer, place a sheet of aluminum foil on top
- DurationOvernight incubation is applied to ensure that digestion will be complete and/or to facilitate the organization of extraction.

Purification of Genomic DNA:
  • Following incubation, dispense Amount250 µL of the Wizard SV Lysis Buffer into each well of the deep-well plate containing lysate

Note
- Lysate must be warm during processing
- Mix each well’s contents by pipetting up and down three times to ensure homogeneity

  • Prepare the Vacuum Manifold (see figure on summary sheet)
  • Place the Binding Plate in the Vacuum Manifold Base
  • Orient the Binding Plate in the Vacuum Manifold with the numerical column headers toward the vacuum port
  • Attach the vacuum line to the vacuum port on the Manifold Base
  • Transfer the tissue lysates to the wells of the Binding Plate
  • Apply vacuum until all of the lysate has passed through the Binding Plate
Note
- Caution: Always place a liquid trap (e.g., vacuum flask) between the manifold and the vacuum pump to avoid damaging the pump with aspirated liquid
- Vacuum pressure should be approximately 508 mBar (or 50.8 kPa) for efficient processing
- To maintain strong vacuum across the wells, cover the plate with adhesive plate sealer
Wash & Dry:
  • Add Amount900 µL of Column Wash Solution (CWA) to each well of the Binding Plate
  • Apply vacuum until the CWA passes through the Binding Plate
  • Repeat two more times for a total of 3 washes with the CWA
  • After the wells have emptied, continue to apply vacuum for an additional Duration00:06:00 to allow the binding matrix to dry
  • Turn off the vacuum
  • Release the vacuum line from the Manifold Base, and snap it into the vacuum port in the Vacuum Manifold Collar
  • Remove the Binding Plate from the Manifold Base
  • Blot by gently tapping onto a clean paper towel to remove residual ethanol and repeat if necessary to remove all residual ethanol
Note
- A fourth wash can be performed if necessary

Elute:
  • Place the 96-Well Deep Well Plate in the Manifold Bed and position the Vacuum Manifold Collar on top
  • Orient the plate with the numerical column headers toward the vacuum port
  • Position the Binding Plate on top of the Manifold Collar
  • Place the Manifold Collar containing the Binding Plate on top of the 96-Well Deep Well Plate sitting on the manifold bed
  • The Binding Plate tips must be centered on the Deep Well Plate wells, and both plates must be in the same orientation
  • Add Amount250 µL of TemperatureRoom temperature Nuclease-Free Water to each well of the Binding Plate and incubate for Duration00:02:00 at TemperatureRoom temperature
  • Apply vacuum until the Nuclease-Free Water passes through the Binding Plate
  • Release the vacuum and remove the Wizard SV 96 Binding Plate
  • Optional: transfer the samples into 1.5 mL tubes

Safety information
- Gently detach the Manifold Collar ensuring the Deep Well Plate stays properly aligned in the Manifold Bed
- In case droplets are visible on the upper edge of the wells, gently tap the plate on the bench to allow them to settle at the bottom


DNA storage
DNA is ready to use immediately or store at:
  • Temperature4 °C for use a few days
  • Temperature-20 °C for use within a few weeks
  • Temperature-70 °C for long-term storage

Note
To store the plate, seal it tightly using a plate sealer

DNA quantification and DNA quality control:
NanoDrop measurement:

  • Use Amount2 µL of elution buffer (without DNA) as a blank to calibrate the NanoDrop and correct for background absorbance
  • To validate the blank, add Amount2 µL of elution buffer onto the NanoDrop pedestal and measure
Equipment
NanoDrop™ One UV-Vis Spectrophotometer
NAME
spectrophotometer
TYPE
Thermo Scientific
BRAND
ND-ONE-W
SKU
https://www.thermofisher.com/order/catalog/product/ND-ONE-W
LINK
Sample Volume (Metric): Minimum 1µL; Spectral Bandwidth: ≤1.8 nm (FWHM at Hg 254 nm); System Requirements: Windows™ 8.1 and 10, 64 bit; Voltage: 12 V (DC); Wavelength Range: 190–850 nm
SPECIFICATIONS
  • To measure DNA concentration of sample, add Amount2 µL of sample DNA onto the NanoDrop pedestal and measure
- Note down the A260/280, A260/230 and concentration (ng/μl)
- or export the data to a USB storage device
Note
- Clean the surface between each read


Qubit Measurement:

  • Ensure the Qubit is calibrated before starting
Equipment
Invitrogen™ Qubit™ 3 Fluorometer
NAME
Accurately measures DNA, RNA, and protein using the highly sensitive fluorescence-based Qubit quantitation assays
TYPE
Invitrogen™ Q33216
BRAND
Q33216
SKU
https://www.fishersci.co.uk/shop/products/qubit-3-0-fluorometer/15387293
LINK
  • Use the ReagentQubit™ dsDNA BR Assay KitThermo Fisher ScientificCatalog #Q32853
- Analyze Amount1 µL of extracted DNA
- Note the concentration (ng/μl)