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. 2025 Jan 7;48(2):100178. doi: 10.1016/j.mocell.2025.100178

Essential resources and best practices for laboratory mouse research

Rosa Haque 1,†, Aysenur Deniz Song 2,†, Jongsun Lee 1, Seung-Jae V Lee 1,⁎, Jae Myoung Suh 2,⁎
PMCID: PMC11847101  PMID: 39788324

Abstract

The laboratory mouse (Mus musculus) is the most widely used mammalian model organism in biomedical and life science research. This concise guide aims to provide essential information to assist researchers new to working with mice, covering topics such as mouse husbandry, maintenance, and available resources for obtaining mouse strains and associated data. Additionally, we discuss ethical considerations, emphasizing the 3Rs (replacement, reduction, and refinement) to ensure responsible and humane research practices.

Keywords: Animal research, Mouse database, Mouse experiments

INTRODUCTION

The mouse has emerged as an indispensable model organism, sharing approximately 85% genetic similarity of protein-coding regions with humans (Mouse Genome, 2002). This remarkable genetic homology, combined with relevant anatomical and physiological characteristics, makes mice excellent models used in different fields of research interest (Kim et al., 2023a, 2023b, 2023c; Lee et al., 2023, 2024; Lim et al., 2023; Suzuki et al., 2023). Furthermore, mice offer several practical advantages, including small body sizes, large numbers of offspring with short gestation time, and relatively shorter lifespan (Bryda, 2013).

The translation of experimental findings from mice to humans requires the reproducibility and validity of experiments, as well as careful monitoring and comprehensive understanding of the mouse model. In this guide, we provide an overview of the resources, tools, and guidelines available for conducting basic mouse experiments. By following established best practices and ethical considerations, researchers can leverage the power of the mouse model to advance scientific knowledge and understanding.

MOUSE STRAINS, RESOURCES, AND FACILITIES

Exploring mouse models first requires obtaining the appropriate strains of interest. Researchers should carefully select specific mouse strains based on the objectives of their study. A variety of mouse strains are available at different research facilities, including The Jackson Laboratory (https://www.jax.org/), Charles River Laboratories (https://www.criver.com/), Inotiv (https://www.inotiv.com/research-models), Janvier Labs (https://janvier-labs.com/en/test-page-search-form-2/), Taconic Biosciences (https://www.taconic.com/), and Cyagen Biosciences (https://apac.cyagen.com/). Additionally, the International Mouse Strain Resource (http://www.findmice.org/index.jsp) provides information on the strain stocks carrying specific alleles of interest that are available worldwide (Eppig et al., 2015).

For further investigations of complex genetic traits, BXD recombinant inbred (RI) mice and Diversity Outbred (DO) mice offer specialized resources. BXD RI mice were systematically created by crossing and inbreeding progeny of two parental strains, C57BL/6J and DBA/2J, providing a reproducible genetic model for mapping quantitative trait loci (QTLs) and understanding gene-by-environment interactions (Mulligan et al., 2017, Peirce et al., 2004). For instance, they have been used to identify QTLs associated with alcohol preference (Rodriguez et al., 1995), blood pressure regulation (Zhao et al., 2017), and cholesterol metabolism (Votava et al., 2024), offering insights into the inheritability and genetic associations of these traits.

For data access and analysis, the GeneNetwork Database (https://fallback.genenetwork.org/) provides comprehensive genotypic and phenotypic data on BXD and other RI lines, supporting QTL mapping and correlation studies. Another valuable resource is the Mouse Phenome Database (MPD; https://phenome.jax.org/) which includes data on BXD strains covering a wide range of phenotypic measures and baseline data.

In addition to BXD mice, DO mice, derived from eight founder strains, maximize genetic variation and closely mimic human genetic variability, making them particularly suitable for high-resolution QTL mapping and the investigation of complex traits (Churchill et al., 2012, Svenson et al., 2012). DO mice have been utilized in research on polygenic diseases, such as obesity (Al-Shaer et al., 2022), type 2 diabetes (Xenakis et al., 2022), and autoimmune diseases (Mayeux et al., 2018).

The Collaborative Cross and DO Reference Database (https://www.jax.org/research-and-faculty/genetic-diversity-initiative/tools-data/diversity-outbred-reference-data) provides genotypic, phenotypic, and sequence data specific to Collaborative Cross and DO populations. Diversity Outbred Database (https://divdb.jax.org/) serves as a repository for data generated from DO mice analyses.

The advent of CRISPR technology has made generating genetically modified mouse models more accessible and efficient, allowing researchers to study specific gene functions or mimic human diseases with unprecedented precision. This has opened new avenues for targeted genetic research and modeling complex diseases where multiple loci contribute to disease susceptibility (Hall et al., 2018).

MOUSE GENOME INFORMATICS

Among the various resources available for mouse research, mouse genomic informatics (MGI) provides a wide range of tools and resources on mouse genetics and genome information (https://www.informatics.jax.org/) (Shaw, 2016). Tools provided by MGI include Mouse Genome Data (http://www.informatics.jax.org) (Eppig et al., 2012), Mouse Phenome Database (https://phenome.jax.org) (Bogue et al., 2020), Gene Expression Database (https://www.informatics.jax.org/expression.shtml), and MouseMine (http://www.mousemine.org). MGI also provides details on mouse strain nomenclature (https://www.informatics.jax.org/nomen/) (Eppig, 2017). Phenotypic outcomes or the genetic basis of complex traits could be predicted by integrating bioinformatics tools such as MPD with experimental designs.

MOUSE HUSBANDRY

Proper mouse care is essential for successful animal research and includes maintaining optimal living conditions, feeding, cleaning, and continuous monitoring of animal health. Understanding the mouse life cycle is essential for effective mouse husbandry and experimental design. Mice have a gestation period of 19 to 21 days, with puberty onset typically occurring by 4 to 6 weeks and sexual maturity reached by 6 to 8 weeks (Hedrich et al., 2004). These life stages are associated with distinct physiological and behavioral changes that researchers must carefully consider when selecting mice for experiments.

Establishing an environment conducive to mouse welfare and reproduction is vital for successful mouse research outcomes (Gerdin et al., 2012). Mouse housing environments substantially influence research outcomes. Specific pathogen–free housing ensures that mice are free from a defined list of pathogens, providing controlled microbiota and enabling reproducible results (Beura et al., 2016). Germ-free housing involves raising mice in sterile conditions, allowing researchers to study host-microbe interactions with precision (Arvidsson et al., 2012). Conventional housing is cost-effective but may expose animals to varying environmental microbes, potentially introducing experimental variability (Hedrich and Bullock, 2004, Slipman, 2007, Voipio et al., 2016). Researchers should select housing conditions based on study goals, considering their impacts on immunological, metabolic, and behavioral parameters.

Other essential factors in mouse husbandry include light-dark cycles, temperature, humidity, nesting materials, enrichment, water supply, and appropriate diets (Pellizzon and Ricci, 2020). The three main diet types—natural ingredients, purified, and chemically defined—are typically sterilized through autoclaving or irradiation to minimize pathogen contamination (Kumar et al., 2021). Detailed information on laboratory mouse diets and general mouse nutrition is available in Weiskirchen et al. (2020). Reputable suppliers of laboratory rodent diets include Teklad (https://www.inotiv.com/laboratory-animal-diets), Research Diets (https://researchdiets.com/), The Jackson Laboratory (https://www.jax.org/), Dyets (https://dyets.com/), and LabDiet (https://www.labdiet.com/).

For detailed information on mouse husbandry practices, researchers can consult resources provided by The Jackson Laboratory (https://www.jax.org/jax-mice-and-services/customer-support/technical-support/breeding-and-husbandry-support/general-husbandry-tips) and The National Centre for the Replacement, Reduction and Refinement of Animals in Research (https://www.nc3rs.org.uk/3rs-resources/housing-and-husbandry-mouse). By carefully considering all aspects of mouse husbandry—from life cycle stages to environmental conditions and nutrition—researchers can enhance the quality and reliability of their animal studies while prioritizing animal welfare.

MOUSE PHENOTYPING

Mouse phenotyping is a critical process for elucidating gene function and associated diseases through the systematic study of physical and biological traits. Phenotypes caused by genetic variations can be measured using behavioral and metabolic tests, and invasive or noninvasive imaging techniques. The frailty index, for example, is a noninvasive approach for assessing health and aging phenotypes of mice (Whitehead et al., 2014). The International Mouse Phenotyping Consortium has established a standardized pipeline for mouse phenotyping, providing annotated phenotypes for many established mouse strains, including various gene knockouts. For guidance on using the International Mouse Phenotyping Consortium web portal (https://www.mousephenotype.org/), refer to Groza et al. (2023). Other key sources include The Jackson Laboratory for detailed procedures of phenotyping and the MPD (https://phenome.jax.org/), which is another repository for extensive mouse phenotypic data.

ETHICAL CONSIDERATIONS

Ethical compliance and animal welfare are critical in mouse research. To ensure humane treatment of animals and reduce reliance on animals, researchers must adhere to the 3Rs principle: Replacement, Reduction, and Refinement (Sneddon et al., 2017). Replacement refers to using alternatives to living animals, whenever feasible. These alternatives not only reduce reliance on animal models but also provide valuable insights into biological processes. Reduction, which can be achieved through noninvasive methods and precise genetic modifications, focuses on minimizing the number of animals without compromising the quality of research. The refinement principle emphasizes minimizing pain and distress in laboratory animals. Researchers should establish humane endpoints based on clearly defined and objective measures, such as limiting tumor size, over 20% body weight loss, severe lethargy, or ulceration (Johns Hopkins University Animal Care and Use, 2024; National Research Council US Committee on Pain and Distress in Laboratory Animals, 1992). These guidelines ensure ethical compliance and improve the reliability of data by reducing stress-related artifacts. Advanced monitoring systems and less invasive techniques also help reduce harm during experiments (Hubrecht and Carter, 2019).

In addition to the 3Rs, researchers must also comply with institutional and national guidelines, such as those set by Institutional Animal Care and Use Committee (Mohan and Huneke, 2019). The following organizations provide essential resources and guidelines for ethical animal research: the National Centre for the Replacement, Reduction, and Refinement of Animals in Research (https://www.nc3rs.org.uk/), the European Commission (https://environment.ec.europa.eu/topics/chemicals/animals-science_en), the National Institutes of Health Office of Laboratory Animal Welfare (https://olaw.nih.gov/policies-laws), the Canadian Council on Animal Care (https://ccac.ca/fr/index.html), and the National Health and Medical Research Council (https://www.nhmrc.gov.au/).

CONCLUDING REMARKS

This guide provides an overview of resources and considerations for conducting mouse experiments, including obtaining specialized strains, utilizing genome informatics platforms, applying husbandry principles, and adhering to ethical standards. This introductory information can help researchers new to mouse models effectively leverage these resources to advance scientific discovery and translation to human health applications. For more detailed guidelines on mouse experiments, users are encouraged to consult additional publications and institutional resources.

Funding and Support

This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (RS-2024-00408712 to S-J.V.L. and RS-2024-00440824, RS-2023-00218616, RS-2024-00346395 to J.M.S.), and the KAIST Venture Research Program for Graduate and PhD students.

Author Contributions

Jae Myoung Suh: Writing—review and editing. Seung-Jae V. Lee: Writing—review and editing, Writing—original draft, Conceptualization. Rosa Haque: Writing—review and editing, Writing—original draft. Aysenur Deniz Song: Writing—review and editing. Jongsun Lee: Writing—review and editing.

Declaration of Competing Interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Seung-Jae V. Lee is an Editor-in-Chief for Molecules and Cells and was not involved in the editorial review or the decision to publish this article.

Acknowledgments

We thank all Lee and Suh laboratory members for their helpful discussion and comments.

ORCID

Rosa Haque: https://orcid.org/0009-0001-9292-028X.

Aysenur Deniz Song: https://orcid.org/0000-0003-0998-9225.

Jongsun Lee: https://orcid.org/0009-0008-9098-6147.

Jae Myoung Suh: https://orcid.org/0000-0001-8097-4662.

Seung-Jae V. Lee: https://orcid.org/0000-0002-6103-156X.

Contributor Information

Seung-Jae V. Lee, Email: seungjaevlee@kaist.ac.kr.

Jae Myoung Suh, Email: jmsuh@kaist.ac.kr.

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