Is it okay to use a secondary antibody as an isotype control for a primary conjugated antibody? I am wanting to use a rat anti-mouse secondary antibody as the isotype control for a rat anti-mouse primary conjugated antibody (they have the same flurophore and are the same isotype). I am worried that the secondary antibody could give me more background than a normal isotype control. (Maybe it would have a higher likelihood of binding to any Fc receptors on my mouse cells, since the secondary antibody is anti-mouse?) I have heard that one can use an irrelevant antibody for a particular tissue type as an isotype control, but I don't have any. It would be great if I could feasibly use the secondary antibody instead, but I don't want to have a higher background than a designated isotype control, as I am looking for a stem cell population that isn't particularly abundant.
Anyone have any knowledge about this? Thanks!