Feb 12, 2024
DNA yield estimation and custom DNA quality evaluation before shotgun metagenomic sequencing
- Benoit Quinquis 1,
- Alexandre Famechon 1,
- nathalie.galleron1,
- Victoria Meslier1,
- Mathieu Almeida2
- 1Université Paris Saclay, INRAE MetaGenoPolis, 78350 Jouy-en-Josas, France;
- 2INRAE MetaGenoPolis
Protocol Citation: Benoit Quinquis , Alexandre Famechon , nathalie.galleron, Victoria Meslier, Mathieu Almeida 2024. DNA yield estimation and custom DNA quality evaluation before shotgun metagenomic sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvo3zzzv4o/v1
Manuscript citation:
Meslier, V.; Menozzi, E.; David, A.; Morabito, C.; Lucas Del Pozo, S.; Famechon, A.;
North, J.; Quinquis, B.; Koletsi, S.; Macnaughtan, J.; et al. Evaluation of an
Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.
Biomolecules 2023, 13, 1505. https://doi.org/10.3390/biom13101505
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: February 09, 2024
Last Modified: May 31, 2024
Protocol Integer ID: 94964
Keywords: ASAPCRN, DNA quantification, DNA quality, shotgun metagenomics
Funders Acknowledgements:
Agence Nationale de la Recherche
Grant ID: ANR-11-DPBS-0001
Aligning Science Across Parkinson's
Grant ID: ASAP-000420
Disclaimer
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Abstract
This protocol describes the procedures used for DNA quantification and a custom DNA quality evaluation before proceeding to shotgun metagenomic seqeuencing.
Image Attribution
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Guidelines
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Materials
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Safety warnings
See safety recommendations from the kits used in this protocol
Ethics statement
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Before start
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DNA quantification
DNA quantification
using the DNA-binding fluorescent Quant-it dsDNA
BR assay
Custom DNA quality estimation
Custom DNA quality estimation
Genomic 50 kb kit by capillary electrophoresis using the Fragment Analyzer, followed by a custom DNA quality analysis
Protocol references
Meslier, V.; Menozzi, E.; David, A.; Morabito, C.; Lucas Del Pozo, S.; Famechon, A.;
North, J.; Quinquis, B.; Koletsi, S.; Macnaughtan, J.; et al. Evaluation of an
Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.
Biomolecules 2023, 13, 1505. https://doi.org/10.3390/biom13101505