C57BL/6J vs C57BL/6N

C57BL/6J carries a mutation in the Nnt (nicotinamide nucleotide transhydrogenase) gene affecting glucose metabolism. C57BL/6N does not have this mutation. Substrains differ in some behavioral phenotypes, seizure susceptibility, and responses to metabolic challenges. C57BL/6N ES cells (JM8 lines) are standard for gene targeting.

For most applications, either substrain works, but consistency within a study is critical. Use C57BL/6N if using standard ES cell targeting resources (EUCOMM, KOMP) that use C57BL/6N ES cells. Use C57BL/6J if matching existing protocols or historical data. Document your substrain choice in publications.

After ES cell targeting and germline transmission, maintain mice on the matching substrain to avoid introducing genetic variability. When ordering mice for breeding or controls, ensure you receive the correct substrain. SNP panels can distinguish C57BL/6J from C57BL/6N and verify substrain identity.

Yes, but this should be avoided as it introduces genetic variability and defeats the purpose of substrain selection. If you have a model on one substrain and need the other, plan for this from the start or use speed backcrossing with marker-assisted selection to convert backgrounds while maintaining the mutation of interest.

Yes. Our documents and reports specify C57BL/6J or C57BL/6N rather than just "C57BL/6" to enable reproducibility and appropriate interpretation. Publications should also specify substrain. This transparency helps researchers make informed decisions and ensures experimental reproducibility.