Data analysis in flow cytometry
Flow cytometry data analysis is built upon the principle of gating. Gates and regions are placed around populations of cells with common characteristics, usually forward scatter, side scatter and marker expression, to investigate and to quantify these populations of interest.
Here we will show what the common flow cytometry graph outputs look like and how in a few simple steps you can identify different cell populations that have been stained with antibodies conjugated to fluorophores.
Before you start your flow cytometry experiment, if possible, it is a good idea to find out as much as possible about the cells and include the right controls. This can be simple things like having an estimation of the size of the cells and if they are likely to change during your experiment. This can be especially useful if you are performing intracellular staining as the fixation and permeabilization process can alter cell size and granularity, resulting in altered forward and side scatter profiles. If your cells have a known marker it can be useful to include this in your staining as it will help identify your cells of interest. Conversely a known negative can also help by allowing you to set negative gates and determine real populations. To find out more about controls go to our dedicated controls in flow cytometry page.