Key Selection Criteria
Tissue Specificity
Does the Cre driver express exclusively in your tissue of interest? Consider both the promoter used and actual expression data from published characterization studies.
- Review published expression patterns and recombination maps
- Consider both intended and unintended expression sites
- Account for embryonic vs adult expression differences
- Verify specificity in your strain background
Expression Timing
When does Cre expression begin? Early embryonic expression may cause deletion before your tissue of interest differentiates, while late expression may miss critical developmental windows.
- Match Cre expression timing to your experimental needs
- Consider developmental stage of target tissue
- Use inducible Cre for precise temporal control
- Account for Cre expression onset vs full activity
Recombination Efficiency
How completely does the Cre driver recombine floxed alleles in target tissues? Variable efficiency can create mosaic deletion patterns that complicate phenotype interpretation.
- Review published recombination efficiency data
- Consider using reporter alleles to assess efficiency
- Higher efficiency is generally preferred
- Account for variation between individual animals
Background Recombination
Does the Cre show any activity outside the intended tissue? Even low level leaky expression can confound results if your gene is essential in other tissues.
- Check for germline recombination (especially with female Cre carriers)
- Review reports of unexpected tissue recombination
- Consider Cre toxicity in expressing tissues
- Assess mosaicism in target and non target tissues
Major Cre Line Categories
Ubiquitous Cre Lines
Express Cre in all tissues, useful for generating global knockouts from conditional alleles.
Tissue Specific Cre Lines
Express Cre in defined tissue types based on endogenous promoter specificity.
Cell Type Specific Cre Lines
Express Cre in specific cell populations within tissues.
Developmental Stage Cre Lines
Express Cre at specific developmental timepoints.
Inducible Cre Systems
Inducible Cre lines provide temporal control over gene deletion, enabling deletion in adult animals or at specific developmental timepoints.
CreERT2 (Tamoxifen Inducible)
Cre fused to modified estrogen receptor. Inactive until tamoxifen administration. Most widely used inducible system.
Advantages
- Tight temporal control
- Wide variety of tissue specific versions available
- Reversible (deletion is permanent, but Cre activity requires continued tamoxifen)
Considerations
- Tamoxifen has estrogenic effects
- Efficiency varies with dose and timing
- Some leakiness possible without induction
Tet Inducible Cre
Cre expression controlled by doxycycline. Can be either Tet On (dox activates) or Tet Off (dox represses).
Advantages
- Reversible control of Cre expression
- Dose dependent expression levels
- No estrogen related effects
Considerations
- Requires two transgenes (tTA/rtTA and TetO Cre)
- Background activity varies by line
- Doxycycline has some biological effects
Cre Line Selection Workflow
Step 1: Define Your Requirements
Specify the tissue(s), cell type(s), and timing for gene deletion based on your experimental questions.
Step 2: Search Available Cre Lines
Use resources like the Jackson Laboratory Cre Portal, MGI, or IMSR to identify candidate lines expressing in your tissue of interest.
Step 3: Review Published Characterization
For each candidate, review published data on expression pattern, recombination efficiency, and any reported issues.
Step 4: Evaluate Specificity and Timing
Assess whether expression pattern matches your needs. Consider both intended and unintended expression.
Step 5: Check Availability and Background
Verify the line is available, and consider whether strain background is compatible with your floxed allele.
Step 6: Plan Validation Experiments
Plan to validate Cre expression and recombination in your specific cross using reporter alleles or PCR based methods.
Common Selection Mistakes
Mistake: Relying solely on promoter name
Solution: Always check actual expression data. Transgenic Cre lines often have expression patterns that differ from the endogenous gene due to position effects.
Mistake: Ignoring germline recombination
Solution: Some Cre lines show germline activity, especially in females. Always breed Cre through males for the first generation and genotype for recombination.
Mistake: Not considering developmental expression
Solution: A Cre that is specific in adults may have broader expression during development. If your gene is essential during development, this can cause unexpected lethality.
Mistake: Overlooking Cre toxicity
Solution: High Cre expression can be toxic independent of target gene deletion. Always include Cre only controls in your experiments.
Mistake: Assuming complete deletion
Solution: Most Cre lines do not achieve 100% recombination. Plan for mosaic deletion and consider using reporter alleles to assess efficiency.
Resources for Finding Cre Lines
Jackson Laboratory Cre Portal
Comprehensive database of Cre driver lines with expression data and availability information.
Mouse Genome Informatics (MGI)
Searchable database of recombinase alleles with links to expression data and publications.
International Mouse Strain Resource (IMSR)
Global database of mouse strains including Cre lines, with source information.
Published Literature
Original characterization papers often contain the most detailed expression and recombination data.
What Researchers Say
“iTL produced four conditional knockout mouse models on our behalf. They have been extremely helpful and informative at all stages of the project; all the way from construct design to breeding strategies and genotyping the new mouse models. I know where to turn when the needs comes up again for another mouse project; it is certainly faster and cheaper than doing this by ourselves.”
— William A. Coetzee, DSc
NYU School of Medicine
“The Hephaestin flox model ingenious has made for us has been great. It has helped generate eight research publications.”
— Joshua Dunaief, PhD, MD
University of Pennsylvania
Need Help Selecting a Cre Line?
Our scientific consultants can help you identify the optimal Cre driver for your conditional knockout project. We can also assist with breeding strategies and validation approaches.