I just started an exosome isolation (from plasma) protocol (by invitrogen) this week and I am having trouble pelleting the cell debris. I first thaw all my samples on ice, then stick them in the centrifuge at 2000 x g for 20 min @ RT. After this step, there is somewhat of a pellet at the bottom (I place all of my microcentrifuge cap hinges on the outside so even if I can’t see the pellet, I still treat it as though there is a pellet). As I am aspirating the supernatant (using either a p1000, p200, or p100) I seem to pick up cell debris right around where the meniscus is located (the debris also comes from the same side of the tube that the pellet is located on). I transferred the supernatant anyway to a new tube because the protocol calls for another centrifugation step at 10,000 x g for 20 min. However, the same problem came up, so I spun it down again at 15,000 x g for 20 min. It still did not fix the problem.
Is there anything I can do to not pick up any cell debris? I would like to refrain from using a smaller pipeteman (less suction) because this would take more time.
Any ideas would be greatly appreciated!