I want to study the transcriptional changes in T cells in the context with TB infection. I have a doubt as whether flow cytometry or Flowcytometry with cell sorter will be the best one to do.
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.