Comparison and Validation of Ichthyoplankton DNA Extraction Methods
Abstract
:1. Introduction
2. Materials and Methods
- I.
- Ichthyoplankton sampling
- II.
- Extraction of nucleic acid
- 1.
- Extraction with EZ1 DSP Virus Kit (Qiagen, Hilden, Germany) and EZ1 Virus Mini Kit (Qiagen, Hilden, Germany)
- 2.
- Extraction with the QIAamp DSP DNA Kit (Qiagen, Hilden, Germany)
- 3.
- Extraction with the Promega Maxwell Kit (Promega Corporation, Madison, WI, USA)
- 4.
- Heat-protocol for direct PCR (Hp-dPCR) (Our protocol)
- III.
- Quantification of nucleic acids
- IV.
- Amplification of nucleic acids
- V.
- Statistical analysis
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Extraction Method | Concentration ng/µL | R 260/280 |
---|---|---|
EZ1 DSP Virus Kit (Qiagen, Hilden, Germany) | 0.8 ± 0.329 | 1.5 ± 0.086 |
EZ1 Virus Mini Kit (Qiagen, Hilden, Germany) | 7 ± 0.243 | 1.3 ± 0.256 |
QIAmp DSP DNA Kit (Qiagen, Hilden, Germany) | 3 ± 0.598 | 1.6 ± 0.092 |
Promega Maxwell Kit (Promega Corporation, Madison, WI, USA) | 50 ± 0.053 | 1.7 ± 0.624 |
Heat-protocol for direct PCR (Hp-dPCR) (Our protocol) | 170 ± 0.717 | 1.8 ± 0.044 |
Kits | Costs/Kit | Costs/Test | Extraction Duration | Required Instruments |
---|---|---|---|---|
EZ1 DSP Virus Kit | * 475.00$/48 tests | 9.89$ | 1 h | EZ1 advanced XL |
EZ1 Virus Kit | * 443.00$/48 tests | 9.23$ | 1 h | EZ1 advanced XL |
QIAamp DNA Kit | * 259.00$/50 tests | 5.18$ | 1 h | QIAcube |
Promega Maxwell Kit | * 750.00$/48test | 15.63$ | 1 h 30 min | Maxwell® RSC |
Hp-dPCR Method | Not on the market 3.00$/test | 3.00$ | <30 min | Water bath |
Extraction Method | Ct (Cycle Threshold) |
---|---|
EZ1 DSP Virus Kit (Qiagen, Hilden, Germany) | ------- |
EZ1 Virus Mini Kit (Qiagen, Hilden, Germany) | ------- |
QIAamp DSP DNA Kit(Qiagen, Hilden, Germany) | 33.87 ± 0.746 |
Promega Maxwell Kit (Promega Corporation, Madison, WI, USA) | 20.54 ± 0.4403 |
Heat-protocol for direct PCR (Hp-dPCR) (Our protocol) | 18.32 ± 0.7043 |
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Lamia, D.; Théophile, U.; Hinde, A.; Mohamed, M.; Tarik, B.; Abdelaziz, S. Comparison and Validation of Ichthyoplankton DNA Extraction Methods. Methods Protoc. 2021, 4, 87. https://doi.org/10.3390/mps4040087
Lamia D, Théophile U, Hinde A, Mohamed M, Tarik B, Abdelaziz S. Comparison and Validation of Ichthyoplankton DNA Extraction Methods. Methods and Protocols. 2021; 4(4):87. https://doi.org/10.3390/mps4040087
Chicago/Turabian StyleLamia, Diouri, Uwiringiyeyezu Théophile, Abdelouahab Hinde, Malki Mohamed, Baibai Tarik, and Soukri Abdelaziz. 2021. "Comparison and Validation of Ichthyoplankton DNA Extraction Methods" Methods and Protocols 4, no. 4: 87. https://doi.org/10.3390/mps4040087