Remember that the center stream will contain any particles that did not pass the discriminator, those that did not fall within a live cell gate according to scatter paramteres, and particles that were aborted because they were in neighboring droplets. Imagine staining human PBMCs with FITC-CD4 and PE-CD8. You could sort FITC+/PE- to the left and FITC-/PE+ to the right. One might think that collecting the center stream would be a good way to recover the B lymphocytes (CD4-/CD8-). If all goes well, all of the B cells will be in the center stream, but they will be in small proportion to all of the particles/cells mentioned in the paragraph above. Furthermore, the dilution factor of the center stream is much, much higher than that of the side streams.
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