Hi Shandi,

      I usually treat the "thick" vibratome slices with 0.3% Triton X-100 for 60min first. Then, incubate them with 4ug/ml DAPI for 60min. Please be sure, he staining should be performed at room temperature. Since I always get stable and intensive staining, you may have a try.

     By the way, are you using frozen slices? If so, you may make a little adjustment of incubation time.

     Good luck.

Hi Shandi,

      I usually treat the "thick" vibratome slices with 0.3% Triton X-100 for 60min first. Then, incubate them with 4ug/ml DAPI for 60min. Please be sure, he staining should be performed at room temperature. Since I always get stable and intensive staining, you may have a try.

     By the way, are you using frozen slices? If so, you may make a little adjustment of incubation time.

     Good luck.

Hej

When I work with 100 um section I use 4nM DAPI in PBS and stained for max 2 min and wash afterwards for 10 min with PBS. You can also add 0.3% Triton X-100 before if needed. For >1 mm (with CLARITY, see link) I use 2 μg/ml DAPI in PBS overnight.

Alternatively, buy an easy kit like NucBlue or a mounting media with DAPI like the Prolong Gold with DAPI. Both are easy to fit into a IHC workflow. 

Good luck

Hi Shandi, You wrote that you use FFPE sections. Before you start with your staining you have at first departaffinate your sections in Xylene and rehydrate them in descending alcohols.After a short rinse in destilled water and PBS or TBS you should put your dye  on the sections for 30 min or longer  at room temperature (check it under the  microscope). By the way, if you need to work with such thick sections why do you embed them in paraffin? It is much easier to prepare froszen sections (after cryprotection in 30%sucrose) and treat them free floating.  Good luck!