Perhaps this is a naive question but I'm relatively new to flow and am trying to learn about the correct way to gate. I am using bone marrow chimera mouse model to assess peripheral immune cell infiltration into the brain. GFP+ bone marrow was used to reconstitute non-GFP recipient animals, so GFP+ cells in the brain are indicative of cells from the periphery. I am interested in having a very general idea of which groups have the most infiltration (i.e. %GFP of parent population) and have the raw data that I'd like to gate myself.

My question is, can the exact same gating be used for each sample? They are different genotypes and done across different days, but they are virtually indistinguishable from each other and in my mind it makes sense to have a consistent definition for what I'm considering a singlet or GFP+. I'm gating out debris, then single cells with FSC and SSC, then gating GFP+. No antibodies are used here, just the GFP from the transgenic line. Thanks!