Looking at this from a Mendelian perspective, we're seeing problems in recent tail snips. We're breeding and genotyping multiple Cre-Lox lines. This week, we have seen WT x Het/Het breeders producing Hom's on the floxed (2nd) allele, and Het/Hom breeders producing WT's, Hets and Homs in a single litter. The floxed allele outcome was the most noticeable and my thoughts ran to the floxed primers as the culprit.
Upon a second run, there were changes in both the Cre and floxed lines, but both adhered to typical breeding schemes as genotyping goes. Breeder genotypes as controls, along with other controls are good and do not change, so the problem seems to be with the new litter snips. My thoughts now leans more towards contamination vs the thermocycler or primers.
I believe (hope) we can duplicate results from the second run (being done today with new snips). My question is what was the likely culprit in this mess? I have issues with it being the thermocycler or the primers, as controls worked fine. But something happened with a professional tech. Any ideas would be helpful.
Jessica
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