Karyotyping is performed to determine the percentage of euploid metaphase chromosomes in the targeted ES cell clones.  A normal diploid mouse chromosome count is 40.  At least 40 spreads should be counted.  If 70% or more of the spreads counts total 40, the clone is considered to more likely contribute to both somatic cell chimerism and to germline transmission.

Karyotyping is strongly encouraged prior to injection of targeted ES cells into blastocysts.  If high percentage of aneuploidy (>50%) are observed among the ES cells of a clone, the core is able to help rescue the ES cell clone by subcloning.  The core currently outsources this service.