How Tissue Specific Knockout Works
This approach enables study of genes that cause embryonic lethality when deleted globally, isolation of cell autonomous gene functions, and dissection of tissue specific phenotypes without confounding systemic effects. A single floxed allele can be crossed to dozens of different Cre driver lines, enabling tissue specific deletion across virtually every organ system from one initial mouse line.
The Two Component System
Floxed (Conditional) Allele
The target gene contains LoxP sites flanking critical exons. The floxed allele functions normally in the absence of Cre recombinase.
Cre Driver Line
A transgenic or knockin line expressing Cre recombinase under a tissue specific promoter. Cre is expressed only in defined cell types.
Deletion Pattern Determination
The tissue specificity of gene deletion is determined entirely by the Cre driver:
Cre Driver Lines by Organ System
Nervous System
Neuroscience Mouse ModelsImmune System
Immunology Mouse ModelsMetabolic Tissues
Cardiovascular System
Cardiovascular Mouse ModelsChoosing the Right Cre Driver
Key Selection Criteria
- Specificity:Does Cre expression match your target population?
- Efficiency:What percentage of target cells undergo recombination?
- Timing:When does deletion occur relative to your experimental question?
- Ectopic expression:Does the Cre driver have off-target expression?
- Cre toxicity:High Cre levels can cause cellular effects independent of target gene deletion
Common Pitfalls to Avoid
- Germline recombination:Some Cre drivers cause deletion in germline, converting conditional to global knockout
- Leaky expression:Low level Cre in non-target tissues
- Mosaic deletion:Incomplete recombination in target population
- Developmental vs adult expression:Embryonic Cre deletes during development; may not reflect adult gene function
Applications
Essential Genes
Tissue specific knockout enables study of genes that cause embryonic lethality when deleted globally. By restricting deletion to non-essential tissues or adult stages, researchers can study gene function without developmental lethality.
Cell Autonomous Function
Tissue specific deletion distinguishes cell autonomous from non cell autonomous gene function. Does the phenotype arise from gene loss in the target tissue, or from secondary effects elsewhere?
Target Validation
Tissue specific knockout reveals where target inhibition would have therapeutic effects and where it might cause toxicity, supporting drug development decisions.
Selected Publications
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
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
Milanick W, Li J, Thomas CI, Al-Yaari M, Guerrero-Given D, Kamasawa N, Young SM Jr 2025. Presynaptic α2δs specify synaptic gain, not synaptogenesis, in the mammalian brain.
Neuron 12(113): p1886-1897.E9
What Researchers Say
“ingenious Targeting Laboratory is highly recommended for generating custom animal models. Past 2 years, we have made 2 conditional knockout mouse lines. All processes of each project were scientifically and professionally handled. Their scientific consulting to initiate the project was superb compared to other companies, and transparency of the project progress reported by project managers was excellent. Their excellency and dedication to meet our needs in a timely manner are invaluable to continuation of our research progress.”
— Hyekyung Plumley, PhD
Warren Center for Neuroscience Drug Discovery
Start Your Tissue Specific Knockout Project
Our scientific consultants are ready to discuss your research requirements and the optimal floxed allele design for your experimental goals. Initial consultation is provided at no charge.
Frequently Asked Questions
Tissue Specific Knockout Insights
Explore Cre driver selection strategies, tissue-specific targeting approaches, and conditional knockout best practices. Expert analysis delivered biweekly.