Positive selection involves targeting the desired cell population with an antibody specific to a cell surface marker (CD4, CD8, etc.). The targeted cells are then retained for downstream analysis.
Negative selection is when several cell types are removed, leaving the cell type of interest untouched. Similar to positive selection methods, cells are labeled with antibodies that target specific cell surface markers or populations. However, in the case of negative selection, the unwanted cells are the ones labelled and then subsequently removed.
Both positive and negative selection approaches have their advantages and disadvantages.
One of the main advantages of positive selection is that isolated cells are highly purified when compared to negative selection. This high purity is due to the specific antibodies used to target a particular cell type. Additionally, sequential isolations can be performed on positively selected cells. Many technologies, however, leave the positively selected cells bound to the antibodies or other labeling agents, which may affect some downstream assays.
On the other hand, negative selection produces targeted cells that are unbound by antibodies. Cell isolation protocols using negative selection are also quicker and easier than positive selection approaches. One disadvantage, though, is that negative selection methods are inherently less pure than positive selection methods, since it is more difficult to target all unwanted cells than one wanted cell population.
The choice to use a positive or negative selection method depends on both your cell population and potential research applications.
Is there a robust selection marker on the surface of the cell type you want to target? If yes, consider positive selection methods. If no, consider negative selection methods.
Could antibodies or other labeling agents attached to your targeted cells affect downstream assays or research applications? If yes, it may make more sense to use negative selection methods. If no, try positive selection methods.