Hello! I would like to design primers for a set of genes involved in apoptosis (p53, BAX, BCL2, etc) using chinese hamster CHO-K1 cell line. However, when I browse UCSC looking for the genes' sequence I find two different genomes: CHO K1 cell line/criGriChoV1 and C_griseus_v1.0/criGri1. The former refers to the actual cell line, whereas the latter refers to the hamster itself.
Which one do you think I should use for designing my primers?
Thanks in advance!
Follow this link maybe helpful
https://genome.ucsc.edu/goldenpath/help/hgTracksHelp.html
regards
The differences between genomes of Chinese hamsters are trivial and highly unlikely to influence primer design for any gene. Even the differences between hamsters, rats and mice should not prevent design of primers that can amplify those genes from any genus/species of rodent. If you do find a polymorphism between the genomes, just make sure that it is not at the very 3' end of your primer. It is not uncommon to make primers that work well for all mammals or all tetrapods or even all vertebrates. So making primers that work for all species of hamsters or all rodents is not a big problem.
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