After filtration, you're left with a solution containing a mixture of organelles. To separate a particular organelle from all the others you use ultracentrifugation.
1. The cell fragments are poured into a tube. the tube is put into a centrifuge (a machine that separates material by spinning) and is spun at a low speed. the heaviest organelles, like nuclei, move to the bottom of the tube. They form a thick sediment at the bottom - the pellet. The rest of the organelles stay suspended in the fluid above the sediment - the supernatant.
2. The supernatant is drained off, poured into another tube and spun in the centrifuge at a higher speed. Again, the heaviest organelles, this time the mitochondria, form a pellet at the bottom of the tube. The supernatant containing the rest of the organelles is drained off and spun in the centrifuge at an even higher speed.
3. This process is repeated at higher and higher speeds, until all the organelles are separated out. Each time, the pellet at the bottom of the tube is made of lighter and lighter organelles.
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