Knockout Approaches
Conventional Knockout
Conventional knockout models provide global gene inactivation from the earliest stages of development. The target gene is disrupted throughout all tissues for the lifetime of the animal. This approach is appropriate when studying genes that are not essential for embryonic development and when whole organism effects are the primary research interest.
Conventional knockouts offer a straightforward path to loss of function phenotypes with shorter project timelines and lower complexity than conditional approaches.
Learn more→Conditional Knockout
Conditional knockout models use the Cre lox system to control where and when gene inactivation occurs. LoxP sites flanking critical exons remain silent until the allele is exposed to Cre recombinase, at which point the target sequence is excised and gene function is lost.
This approach is essential when global knockout causes embryonic lethality, when tissue specific gene function is the research focus, or when temporal control over gene deletion is required. Conditional knockouts provide maximum experimental flexibility from a single allele design.
Learn more→Tissue Specific Knockout
Tissue specific knockouts combine conditional (floxed) alleles with Cre driver lines that express Cre recombinase in defined cell populations. Gene inactivation is restricted to tissues where Cre is active, while gene function is preserved in all other cells.
Common applications include studying gene function in specific organs, investigating cell autonomous versus non cell autonomous effects, and avoiding confounding systemic phenotypes that can mask the biology of interest.
Learn more→Inducible Knockout
Inducible knockout models add temporal control to conditional systems. Tamoxifen inducible CreERT2 or doxycycline regulated systems allow researchers to trigger gene deletion at specific developmental stages or in adult animals.
This approach enables studies of gene function after normal development, investigation of acute versus chronic loss of function phenotypes, and modeling of disease onset in mature animals.
Learn more→Choosing Between Knockout Strategies
Not sure which approach is right for your research? Our knockout strategy guide walks through the decision framework, or schedule a consultation with our scientific team.
Technical Approach
Allele Design
ingenious targeting laboratory designs knockout alleles based on your specific experimental requirements. Critical exons are selected for loss of function after deletion. For conditional alleles, LoxP sites are positioned to preserve normal gene expression in the absence of Cre while supporting null phenotypes after excision.
Selected Publications
Knockout models generated by ingenious targeting laboratory:
Salzbank J, Lacaille H, Gaby J, O'Reilly JJ, Kissner M, Vacher CM, Penn AA. (2025).
Microglia alter sex-specific cerebellar myelination following placental hormone loss ↗Nat Commun 16(1): 9846
Reinartz DM, Escamilla-Rivera V, Shao M, Tribble SL, Caulin C, Wilson JE. (2025).
Impact of absent in melanoma 2 on head and neck squamous cell carcinoma development ↗J Immunol. vkaf224
Wang L, Noyer L, Jishage M, Wang YH, Tao AY, McDermott M, Gando I, Sidhu I, Hu K, Zhong L, Sun K, Drmic D, Kaufmann U, Feske S. (2025).
CLNS1A regulates genome stability and cell cycle progression to control CD4 T cell function and autoimmunity ↗Sci Immunol 108(10): eadq8860
What Researchers Say
“I'd like to thank the ingenious team for making this mouse for us. We are so excited! Everyone at ingenious has been wonderful to work with throughout the entire process. We will definitely be in contact the next time we need a mouse!”
— Julia Maxson, PhD
Knight Cancer Institute, Oregon Health & Science University
Knockout Model Selection Strategy
When to Choose Conventional Knockout
Conventional knockout models are optimal when complete gene deletion throughout the organism is desired and tissue specific or temporal control is not required. These models are faster to generate, typically more cost effective, and provide definitive loss of function phenotypes.
Conventional knockouts are ideal for studying genes with non essential functions, genes where global deletion does not cause embryonic lethality, and research applications where tissue specific effects are not a concern.
When to Choose Conditional Knockout
Conditional knockout models using the Cre lox system provide spatial and temporal control over gene deletion. These models are essential when global gene deletion causes embryonic lethality, when tissue specific gene function needs to be studied, or when temporal control of gene inactivation is required.
Conditional knockouts enable researchers to study gene function in specific tissues at defined developmental stages or in response to experimental treatments, providing flexibility that conventional knockouts cannot offer.
Project Planning Considerations
When planning a knockout project, consider your long term research goals. If multiple research applications are anticipated, a conditional knockout provides maximum flexibility. If the research question is focused and well defined, a conventional knockout may be more efficient.
ingenious targeting laboratory's scientific consultants work with researchers to select the optimal knockout strategy based on research goals, timeline, and budget considerations.
Knockout Comparison
| Factor | Conventional | Conditional |
|---|---|---|
| Gene essentiality | Non essential genes | Essential or pleiotropic genes |
| Research focus | Whole organism | Tissue specific |
| Temporal control | None (constitutive) | Available with inducible Cre |
| Allele flexibility | Single configuration | Multiple derivative alleles |
Advanced Knockout Strategies
Knockout First Allele System
The knockout first allele system provides maximum flexibility by generating a single targeting event that can produce multiple derivative alleles. This approach is cost effective when multiple research applications are anticipated from a single model.
Knockout first alleles can be converted to conditional knockouts, reporter knockins, or other configurations through breeding with appropriate recombinase lines, providing researchers with multiple options from a single initial investment.
Tissue Specific Knockout Considerations
When planning tissue specific knockouts, careful selection of Cre driver lines is essential. The Cre line must express in your target tissue but not in tissues where gene deletion would cause confounding effects or embryonic lethality.
Start Your Knockout Project
Our scientific consultants are ready to discuss your research requirements and determine the optimal knockout strategy for your experimental goals. Initial consultation is provided at no charge.
Key Terms
Understanding the terminology used in knockout mouse model generation helps you communicate effectively with our scientific team and interpret project documentation.
Knockout
A gene targeting strategy that inactivates a gene by deleting critical sequences, disrupting the reading frame, or inserting stop sequences.
Null Allele
An allele that produces no functional gene product, created by deleting critical exons or introducing premature stop codons.
Homologous Recombination
A precise DNA repair mechanism where a sequence is exchanged between two similar DNA molecules. Used to insert modifications at specific genomic locations.
ES Cells
Embryonic stem cells that can contribute to all tissues including the germline when injected into host blastocysts.
Knockout Resources & Tools
Download our free guides and use our interactive tools to plan your knockout project.
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Frequently Asked Questions
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