If you want to sort these populations and then do the genetic analysis it will be a challenge to sort T regs as they are Foxp3 positive for which you have to do intracellular staining. For intracellular staining you have to fix and permeablize the cell. once u have poked holes in a cell u cannot sort them. Unless u are working with Foxp3 GFP reported mouse where you dont have to go intracellular. But if u r working with human samples it would be not possible.

Another trick could be to not to use GITR instead of FOXP3 as a marker for T regs. But u will have to show that the level of expression of both GITR and FOXp3 is equivalent. I dont know if reviewers will accept it or not. But I have seen a couple of papers doing that.

I meant 'to use GITR instead of Foxp3'. Sorry it was a typing error