How to Choose What JAX Genotyping Protocols To Use

You've received your new-to-you JAX strain and you're ready to start genotyping! You navigate to the strain datasheet and find the genotyping protocols section, but lo and behold, there are multiple protocols listed – they have different names, use different kinds of PCR, and different primer sequences. Do you need to use all of them, or just one of them? This article will describe the reasons why there may be multiple protocols listed, and how to go about choosing which one(s) you need.

Need to know how to find the genotyping protocol for your strain? Please refer to How to Find a JAX Genotyping Protocol.

There are 4 reasons why there may be multiple protocols listed for a JAX strain

Type Description Example How to Choose

Multiple Alleles

Protocols for different alleles

A strain may carry multiple alleles (i.e. double or triple mutants), and there may be protocols for unwanted or background alleles

Determine which alleles you need to genotype for your JAX strain

Type of PCR

Protocols for different types of PCR

For a single allele, you may see protocols for standard PCR, QPCR, and Probe/Endpoint analysis among others

Determine which genotypes you need to differentiate, and what PCR you are capable of performing in your facility


Protocols are either specific or generic

There may be protocols that are specific to that allele, and protocols that are generic (i.e. cre or neo)

Determine which genotype you need to differentiate, and what other strain(s) you may breed to


Multiple similar protocols

Multiple protocols may be similar, however with different primer sequences that anneal to a different region of the allele

Consider trying both protocols to see which primer set works better with your PCR setup