Working with the side population can be very tricky. There is very high variability in the assay since it is a functional assay and it is difficult to get uniform results each time. A lot of parameters that can impact SP isolation are not mentioned in published papers. Apart from the standard protocol that is found in various publications, I will suggest you keep the following parameters in mind when you do the assay:
1. Shaking during the Hoechst staining: During the 90 minute period in which the cells are stained with the Hoechst dye, make sure that the cells are constantly shaking at 37 degrees. Cancer cells (particularly the H460 cell line) tend to settle very rapidly which can cause poor staining giving a false high percentage of the SP.
2. Keep sample on ice while sorting: Immediately after the 90 minute staining, the cells should be constantly kept on ice. If the temperature increases, the ABC transporters become active and you will see a rise in the SP percentage while you're sorting (this is especially true if you need to sort large numbers and if the sample holder in the cell sorter is not kept at a low temperature).
3. Cell concentration and sample volume during staining: Cell concentration during the staining is critical. Make sure you have no more or less than 1 million cells per ml when staining, also do not use more than 2 ml of the cell solution per 15 mL falcon tube. If you increase the volume in the tube, the cells are shaken less effectively and consequently you will get a SP percentage higher than normal.