Feb 12, 2025
Protocol for DNA extraction and shotgun metagenomic sequencing for the study of the mice digestive microbiota
- Victoria Meslier1,
- Mallia Geiger1,
- Yani Ren1,
- Alexandre Famechon1,
- Marine Gilles1,
- Aymeric David1,
- Christian MORABITO1,
- Benoit Quinquis1,
- Mathieu Almeida1
- 1Université Paris Saclay, INRAE MetaGenoPolis, 78350 Jouy-en-Josas, France
Protocol Citation: Victoria Meslier, Mallia Geiger, Yani Ren, Alexandre Famechon, Marine Gilles, Aymeric David, Christian MORABITO, Benoit Quinquis, Mathieu Almeida 2025. Protocol for DNA extraction and shotgun metagenomic sequencing for the study of the mice digestive microbiota. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6x5wklqe/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: February 08, 2024
Last Modified: February 12, 2025
Protocol Integer ID: 94896
Keywords: ASAPCRN, metagenomics, murine, microbiota, DNA extraction, mapping, high throughput sequencing
Funders Acknowledgements:
Agence Nationale de la Recherche
Grant ID: ANR-11-DPBS-0001
Aligning Science Across Parkinson's
Grant ID: ASAP-000420
Abstract
This protocol describes the procedures for whole DNA extraction, high throughput sequencing, metagenomic read mapping and bioinformatical pre-processing to determine the microbial composition and functional potential of the mice digestive microbiota.
Attachments
Guidelines
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Materials
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Safety warnings
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Ethics statement
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Before start
Ensure proper sampling and samples conservation before proceeding to DNA extraction.
DNA extraction and high throughput sequencing
DNA extraction and high throughput sequencing
DNA extraction was performed as described in dx.doi.org/10.17504/protocols.io.dm6gpjm11gzp/v1, with modifications.
WGS high throughput sequencing was described in [1]
Read Mapping and Bioinformatics
Read Mapping and Bioinformatics
Read mapping was performed using the parametres described in the attached document on the MIMIC2 mice gene catalog : https://doi.org/10.15454/L11MXM
Data preprocessing was performed as described in the attached document
Protocol references
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[fileUNF]
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