Q: There is no protocol listed for my strain. What do I do?

A: Contact JAX Technical Support to see if there are any protocols that are not listed on the website. Genotyping protocols are not available for all JAX® Mice strains. If none are available, you can check the primary reference(s) from the investigator who donated the strain or develop your own assay based on information found in the literature.

Q: Why is there not a standard PCR listed for this JAX strain?

A: Not all strains can be genotyped using standard PCR. Some strains will have point mutations that are too small to detect with standard PCR, and may require a Probe-based assay or sequencing.

Q: Why is this standard PCR not capable of differentiating hemizygous from homozygous transgenic animals?

A: Transgenes integrate randomly into the genome, and for most transgenic strains we do not know where in the mouse genome the transgene is located. Without this information, it is not possible to design a wild type primer set. Standard PCR protocols for transgenic strains typically have one primer set to test for the presence or absence of the transgene, and one primer set for an internal positive control (IPC). PCR protocols with these primer sets are not capable of differentiating hemizygous and homozygous animals because they can only determine presence/absence of the transgene. To differentiate hemizygous and homozygous transgenic mice, typically a QPCR protocol must be used.

Q: The genotyping protocol that I have been using for years is no longer on the website. What happened to it?

A: JAX genotyping protocols are often optimized throughout the years. We may develop a new protocol that is more specific, more robust, or for a different type of PCR. Older protocols may be archived when a new version is made available.

Q: If the protocol I choose isn’t working well, should I switch to a different one?

A: Not necessarily. JAX protocols are optimized for our high-throughput facility, and often require optimization to work well with a different PCR setup. Please review our JAX Genotyping Troubleshooting Guide for assistance. If your genotyping is still not successful, you could consider switching to a different protocol if one is available.