I want to breed a transgenic mouse strain that expresses a transgene as well as the thy1.1 congenic marker. I will breed the transgenic mouse with a thy1.1 mouse on the same background, and I would like to determine if the litters express the transgene and are also homozygous for thy1.1. Can this be done by FACS, where thy1.1 homozygotes can be distinguished from thy1.1/thy1.2 heterozygotes?
In my opinion, you may be able to. We used to do adoptive transfer experiments in congenic strains and used to track the endogenous vs transferred cells using flow. You could in theory, use the same principle. You could collect and stain peripheral blood cells with CD90.1 and CD90.2. Mice that are het would have cells that express both. Mice that are homo for CD90.1 should not have cells that stain +ve for CD90.2. Would be a good idea to test this first. If it doesn’t work, you would have to use PCR to distinguish between homo and het mice.