If you want to try density gradient centrifugation, you should be aware that granulocytes may change their density in response to some stimuli so that at least some of your neutrophils might not be where you expect them in your gradient. If you can also go for protein rather than RNA (which might be more informative), you can also try FACS staining for your protein (together with CD16 for neutrophils) followed by RBC lysis and then analyse protein expression by FACS. This way you minimise handling of the cells after stimulation.

Another thing might be of interest for you: Millipore offers new reagents (http://www.millipore.com/life_sciences/flx4/smartflare_live_cell_rna_detection) that allow specific RNA detection in live cells using FACS. However, so far they don't have so many probes yet and I do not know whether they work with neutrophils (I haven't tried them at all). If you decide to try, I would be interested in hearing about your experience.

Good luck!

Thanks for the reply Christina. I will be looking at some markers via FACS, but also wanted to be able to save stimulated samples for future analysis or confirmation of the FACS results. Good to know about the change in granularity, though.