C57BL/6: The Research Standard
The C57BL/6 mouse is the most widely used inbred strain for biomedical research and the reference strain for the mouse genome sequence. C57BL/6 backgrounds are preferred for most knockout, knockin, and conditional allele projects due to extensive phenotypic characterization, broad research community adoption, and compatibility with the majority of Cre driver lines.
Understanding the differences between C57BL/6 substrains is essential for experimental design. The two major substrains, C57BL/6J and C57BL/6N, diverged decades ago and carry distinct genetic variants that affect metabolism, behavior, and other phenotypes.
Research Community Standard
Most commonly used background for genetically engineered mouse models, providing extensive baseline phenotypic data for comparison and compatibility with published Cre driver lines.
Cre Driver Compatibility
The majority of tissue specific Cre driver lines are maintained on C57BL/6 backgrounds, enabling direct crosses without introducing mixed background effects.
Genome Reference
C57BL/6 is the reference strain for the mouse genome sequence, ensuring accurate targeting design and comprehensive genetic characterization.
Breeding Performance
Good maternal behavior, moderate litter sizes (5 to 7 pups), and compatibility with standard breeding protocols make C57BL/6 reliable for colony establishment.
C57BL/6 Substrain Comparison
The two major substrains carry distinct genetic variants that affect metabolism, behavior, and other phenotypes. Selecting the appropriate substrain ensures your model aligns with published literature.
| Characteristic | C57BL/6J (Jackson) | C57BL/6N (NIH) |
|---|---|---|
| Nnt Status | Mutant (deleted) | Wildtype (intact) |
| Insulin Secretion | Impaired | Normal |
| Diet Induced Obesity | More susceptible | Less susceptible |
| rd8 Retinal Mutation | Absent | Present in some colonies |
| IKMC Allele Compatibility | Requires backcrossing | Native background |
| Historical Literature | More extensive | Growing rapidly |
| Best For | Behavioral, oncology studies | Metabolic studies, ES cell targeting |
Choosing Between Substrains
- Consider Nnt status when studying metabolic phenotypes, insulin secretion, or diabetes models
- Consider rd8 when studying retinal or visual phenotypes (verify colony status)
- For IKMC alleles, C57BL/6N maintains pure background without backcrossing
- For literature comparison, use the substrain matching your reference publications
Applications by Research Area
Metabolic Research
Strain background significantly impacts metabolic phenotypes:
- Diet induced obesity: C57BL/6J develops more pronounced obesity and glucose intolerance on high fat diet
- Insulin secretion studies: C57BL/6N preferred when studying beta cell function due to intact Nnt
- Diabetes models: Background choice affects baseline glucose homeostasis and disease susceptibility
Document substrain in publications and consider Nnt genotype when interpreting metabolic data.
Metabolic Disease Mouse ModelsNeuroscience Research
Behavioral and neurological phenotypes vary between substrains:
- Anxiety related behavior: Substrains differ in open field and elevated plus maze responses
- Learning and memory: Subtle differences in some cognitive paradigms
- Retinal studies: Verify rd8 status in C57BL/6N when studying visual system
Immunology Research
C57BL/6 mice carry the H2b MHC haplotype and display Th1 biased immune responses:
- Well characterized immune cell populations
- Extensive reagent availability (antibodies, tetramers)
- Compatible with most syngeneic tumor models
Oncology Research
C57BL/6 is compatible with common syngeneic tumor cell lines and provides immunocompetent background for immuno oncology studies:
- B16 melanoma, MC38 colon carcinoma, LLC lung carcinoma compatibility
- Suitable for immune checkpoint studies
- Well characterized tumor microenvironment responses
BALB/c Mouse Background
BALB/c mice are particularly valuable for immunological studies, syngeneic tumor models, and research where the strain's unique characteristics provide experimental advantages. The albino (c) designation reflects the tyrosinase mutation that eliminates pigmentation.
Immunological Characteristics
- Th2 biased immune response (IL4, IL5, IL13 production)
- Excellent for allergic disease and asthma models
- Strong antibody production (monoclonal antibody source)
- Functional complement system
Research Applications
- Syngeneic tumor models: CT26, 4T1, RENCA, A20 compatibility
- Allergy and asthma: Ideal for allergic airway disease
- Infectious disease: Well characterized pathogen responses
- Autoimmune disease: Lupus, arthritis models
Physical Characteristics
- Albino with pink eyes and white fur
- Docile temperament, easy to handle
- Litter sizes: 5 to 8 pups
- Relatively low body fat compared to C57BL/6
C57BL/6 vs BALB/c: Key Differences
C57BL/6
- Immune bias: Th1 (IFN-γ, TNF-α)
- Metabolic: Susceptible to diet induced obesity
- Behavior: Lower anxiety in standard tests
- Tumor models: B16, MC38, LLC
- Cre drivers: Extensive library available
- Use for: Standard research, metabolic studies, behavior
BALB/c
- Immune bias: Th2 (IL-4, IL-5, IL-13)
- Metabolic: Resistant to diet induced obesity
- Behavior: Higher anxiety in standard tests
- Tumor models: CT26, 4T1, RENCA, A20
- Cre drivers: Limited compared to C57BL/6
- Use for: Immunology, allergy, infectious disease
Technical Considerations
Backcrossing Requirements
When targeted alleles are generated on 129 strain backgrounds, backcrossing to C57BL/6 is required to achieve congenic status:
| Generation | Background Purity |
|---|---|
| N1 | 50% |
| N5 | 97% |
| N10 | 99.9% |
Speed congenic approaches using marker assisted selection can achieve N10 equivalent purity in fewer generations.
Learn About Backcrossing ServicesBreeding Performance
C57BL/6 mice have moderate breeding performance compared to outbred strains:
- Average litter size: 5 to 7 pups
- Weaning age: 21 days
- First litter typically at 10 to 12 weeks of age
- Good maternal behavior
- Compatible with SPF housing conditions
- Moderate lifespan (approximately 24 to 30 months)
Plan breeding timelines accounting for these parameters when estimating cohort development schedules.
Other Strain Backgrounds
129 Strains
Commonly used for ES cell derivation due to excellent germline transmission. Multiple substrains exist (129S1, 129S4, 129Sv). Often backcrossed to C57BL/6 for pure background.
FVB/N
Excellent for transgenic generation via pronuclear injection due to large, visible pronuclei. Good breeding performance with large litters. Carries rd1 retinal degeneration allele.
DBA/2
Used for specific research applications including glaucoma models, hearing loss studies, and neuroscience research. Develops age related hearing loss and glaucoma susceptibility.
NOD (Non Obese Diabetic)
Spontaneously develops autoimmune diabetes. Used as background for autoimmune disease models and immunodeficient derivatives (NSG, NOG). Requires special husbandry.
How to Choose Your Strain Background
1. Consider Your Research Application
Match strain characteristics to your research question. Metabolic studies may benefit from specific substrain selection. Immunology research should consider Th1/Th2 bias.
2. Review Published Literature
Use the same background as reference publications to enable direct comparison. This is especially important for novel phenotype characterization.
3. Verify Cre Driver Compatibility
If generating conditional alleles, ensure your chosen Cre driver is available on compatible background or plan backcrossing strategy.
4. Consult with Our Scientific Team
Our team provides expert guidance on strain selection at no additional cost. We help you navigate substrain differences, backcrossing requirements, and timeline considerations.
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