Well, what exactly do you want to do? there are several techniques to use:

http://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CDEQFjAB&url=http%3A%2F%2Fwww.chemometec.com%2FRenderers%2FShowMedia.ashx%3Fid%3D23dbf708-6836-4a1f-9491-662cd23aff64&ei=LJ9hUMmANcXPtAat5oBI&usg=AFQjCNE7TzkCBhuKYwaHGkd-QteeGKiWPg

or even for sorting:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677894/

http://www.springerlink.com/content/k850250x060w504x/

Thanks for your answer. Our goal is to investigate if in a species of rodent (genus Akodon) the variation in chromosome number among individuals is accompanied by loss or gain of genetic material or results from a rearrangement of the genetic material. We count with a Facsverse (no sorter) and we would like to compare the amount of the DNA within a single cell of different individuals.

We also work on a Verse, which is quite nice. Check out BDs recommendations for DNA measurements with FACS Verse:

http://www.bdbiosciences.com/documents/BD_Instruments_FACSVerse_CellCycle_DNA_Analysis_AppNote.pdf

Have you contacted BD. They are usually quite responsive with such issues.

I just talked to the support staff of BD, thanks for the tip. The protocol is becoming clear. It seems that we will use 7AAD in permeabilized cells and make a relative quantification among individuals.