Lungs are fixed by PFA and embeded in OCT and stored at -80oC. I am using the general protocol of abcam (http://www.abcam.com/protocols/immunostaining-paraffin-frozen-free-floating-protocol) to stain frozen sections of mice lungs and I get auto-fluorescence.
Yavuz,
Autofluorescence is always a problem with IF staining. One of the things that can cause a great deal of autofluorescence is the fixing and permeabilizing agent used, but PFA is a good choice for this, as compared to methanol. Another common cause of autofluorecence is the presence of RBCs in the sample. Although this cannot be completely avoided, it can be reduced if you perfuse the animal with saline upon sacrifice before harvesting the tissue. You can never remove all the RBCs, but perfusing does help.
If you can't decrease the autofluorescence enough even with settings on your microscope/camera setup, then can you use IHC instead? If you use adequate peroxide to quence the endogenous peroxidase activity (I use 3% peroxide in methanol--10x the concentration in the abcam protocol) then you can get very clear staining and be able to see the structure in the tissue.
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