Annexin-V staining - (Jun/09/2011 )

I am new to flow cytometry analysis, sorry if my question seems stupid. i am working with thymi and going to administer hidrocortisone to mice. i need to detect apoptosis by AnnexinV-FITC staining. But during thymocytes isolation I will damage cells (control cells also go through the same procedure), resulting more than expected number of PI +ve and annexin +ve cell. What do you think? I need advice before I do my research. Thank you in advance.
Miss S

In thymus you ALWAYS have a huge % of apoptotic cells. It is normal.