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Short answer: C57BL/6 (also written C57BL6, B6 or “black 6”) is a widely used inbred mouse strain, and the name covers several genetically distinct substrains. The two most common are C57BL/6J, held at The Jackson Laboratory, and C57BL/6N, derived from a 1951 colony sent to the NIH. They differ at more than 200 variants, so a methods section that says only “C57BL/6 mice” leaves the animals under-specified.
This is general reference information for researchers, lab staff and animal-facility and procurement teams. It is not veterinary, regulatory or protocol advice; your IACUC and vendor documentation govern your own work.
What is C57BL/6?
C57BL/6 is an inbred mouse strain with a black coat. The lineage traces to Abbie Lathrop’s mouse breeding farm in Granby, Massachusetts. In 1921, C.C. Little, a student of Harvard geneticist William Castle, crossed female mouse 57 with male mouse 52 from Lathrop’s stocks, producing the “C57 Black” (C57BL) line. Little established the C57BL/6J substrain at The Jackson Laboratory in 1948, and in 1951 a colony went to the NIH, where it became C57BL/6N and was later distributed to commercial vendors including Charles River, Harlan Sprague Dawley and Taconic Farms (Goldstein and Wagers, 2018).
Why it became the reference strain
C57BL/6J was chosen as the reference substrain by the Mouse Genome Sequencing Consortium and by the Allen Brain Atlas, so much of the genomic and neuroanatomical reference data in mouse biology describes this animal (Goldstein and Wagers, 2018). The International Knockout Mouse Consortium, by contrast, disrupted many genes on a C57BL/6N background, so knockout resources and the reference genome do not share a substrain.
C57BL/6J vs C57BL/6N: what differs and why it matters
Both substrains are “C57BL/6”, but they have been bred apart since 1951. The differences below are the ones documented in the two sources cited at the end of this page.
| Difference | Substrain affected | Consequence for study design |
|---|---|---|
| Nnt: in-frame deletion of exons 7-11, so no Nnt protein | C57BL/6J | Linked to abnormal glucose homeostasis in males. On a high-fat diet, 6J males gained more weight, had more adiposity and worse glucose intolerance than 6N males, so metabolic and diet-induced obesity work needs the correct substrain. Reduced ROS scavenging was also reported in hematopoietic progenitors, with weaker short-term blood reconstitution than 6N. |
| Crb1 (rd8) mutation | C57BL/6N | Causes spots of photoreceptor degeneration in the fundus. It can interfere with experiments that depend on vision or that characterize mutations expected to affect vision. |
| Cyfip2 mutation | C57BL/6N | Reported as linked to a reduced cocaine response. |
| Snca deletion (alpha-synuclein gene) | C57BL/6JOlaHsd only | Not carried by other B6 substrains; the deletion has not been shown to affect spatial learning and memory, but it could matter for Parkinson’s disease studies. |
Mixing substrains can change a result. The Jackson Laboratory blog post cited below describes an acetaminophen liver-injury study in which a Jnk knockout looked protective when compared with the wrong control substrain but hepatotoxic when compared with the appropriate one. The practical rule both sources give is to confirm the substrain and use matching controls.
How to read the name: a nomenclature decoder
- C57BL / C57BL/6 / c57bl6 / c57bl 6: “C57BL” is the older line from the 1921 cross; the “/6” denotes the sub-line descended from it. Spaces and slashes in searches (c57bl 6, c57bl6) refer to the same strain name.
- C57BL/6J, B6J: the Jackson Laboratory substrain; the J is the laboratory code.
- C57BL/6N, B6N: the NIH-derived substrain; the N is the NIH code. Vendor-specific lines such as C57BL/6NCrl carry an additional laboratory code.
- C57BL/6JOlaHsd: a 6J-designated line that carries the Snca deletion not seen in other B6 substrains.
- “C57BL/6 mice”, “B6”, “black 6”: informal shorthand. None of these tells a reader which substrain was used.
Common reporting practice for resources is to record a persistent identifier alongside the name; see the RRID (Research Resource Identifier) definition. For where mouse strain data are curated, see the comparison of model-organism databases including MGI.
What are C57BL/6 mice used for?
C57BL/6 is used as a background strain for genetically modified mice and as a wild-type comparator. The sources above tie specific substrain properties to vision research (Crb1), metabolic and diet-induced obesity studies (Nnt), stem-cell and transplantation work (Nnt and ROS handling), neuropharmacology (Cyfip2) and Parkinson’s disease models (Snca). Because the reference genome and brain atlas use 6J while many knockout resources use 6N, the substrain choice affects how results line up with public reference data.
A reporting and specification checklist
Goldstein and Wagers cite a survey by Fontaine and Davis (2016) finding that more than half of published reports using genetically modified mice did not specify the C57BL/6 substrain used, and call for careful and transparent accounting of substrains. A checklist that follows from the two sources:
- Write the full substrain name (for example C57BL/6J or C57BL/6N), not “C57BL/6” or “B6”.
- Record the source of the animals, since substrains are distributed by different vendors and colonies.
- Use controls of the same substrain, and ideally the same source, as the experimental animals.
- Check the substrain against the phenotype under study (vision, glucose handling, Parkinson’s-related work) before choosing it.
- Carry the same substrain information into the animal use protocol, so approval, ordering and the published methods match. See NSG mice for another strain where background matters, and recombinant inbred lines for how inbred strains are used in genetic mapping.
Common misunderstandings
- “C57BL/6 is one uniform strain.” It is a family of substrains with more than 200 documented variants between 6J and 6N.
- “C57BL and C57BL/6 are interchangeable.” C57BL is the older line; C57BL/6 is a specific sub-line.
- “The vendor name does not matter.” The 6N lines distributed by commercial vendors descend from the NIH colony, and the substrain code carries information a reader needs.
FAQ
What are C57BL-6 mice used for?
They serve as a reference inbred strain, a common background for genetically modified mice and a wild-type comparator, in fields including metabolism, vision, neuroscience and hematology. Which substrain is suitable depends on the phenotype, as in the table above.
How much do C57BL/6 mice cost?
Prices are set by vendors and vary with substrain, age, sex, quantity and shipping. This page does not quote prices; use a vendor quotation for your exact specification.
Are C57 mice aggressive?
The sources used for this page do not make a claim about aggression in C57BL/6 mice, so none is made here. Group-housing behaviour such as barbering is covered in barbering in mice and what an IACUC protocol should require.
What is special about BALB/c mice?
BALB/c is a separate inbred strain, not a substrain of C57BL/6. This page covers C57BL/6 only; consult the strain datasheet from your vendor or the Mouse Genome Informatics inbred strain pages for BALB/c characteristics.
Is C57BL/6 the same as C57BL/6J?
No. C57BL/6J is one specific substrain. C57BL/6 without a suffix does not tell the reader whether the animals were 6J, 6N or another substrain.
Sources
- Goldstein, D. and Wagers, A.J. “What’s in a (Sub)strain?” Stem Cell Reports 2018;11(2):303-305. doi:10.1016/j.stemcr.2018.07.011 (PMC6094162). Read 2026-11-07.
- The Jackson Laboratory blog, “Three ways a B6J mouse differs from B6N, and why it should matter to you” (October 2013), jax.org/news-and-insights/jax-blog. Read 2026-11-07.
