Hey, I know this is an old post but just in case you are still interested, I do wholemount staining with skin and adipose tissue, and it works well with the following protocol.
I think it's best to use non-fixed, and just have a very light fixing step with Acetone, that way you can skip antigen retrieval steps. What I do is get a 96 well plate, throw the tissue in PBS at the top, and fill all the wells with the solutions you need for each step. This is actually much easier than working with slides, no more blotting away solutions, you just pick the tissue out with tweezers and move it down a row.
1. Dissect tissue and finely mince in 1x PBS (it's easy to cut thin slices if the tissue is frozen, you work on ice and use a razor or microtome blade).
2. Fix tissue for 30 min, RT on rotating platform (-20C Acetone)
3. Wash 3 times, first wash with 50 mM Glycine 5 min, then 2x 10 min in PBS (Glycine to reduce bg).
4. Permeabilize cells and block non-specific binding in 1 mL B1 buffer at RT on rotating platform (1 hour)
5. Incubate tissue with appropriate dilution of primary antibody in B1 buffer at 4 ˚C on shaking incubator o/n
6. Wash 3 times with 1 mL B2 buffer, 10 min on rotating platform
7. Incubate with appropriate dilution of secondary antibody in B1 buffer and DAPI/DRAQ5/ToPro/Bodipy...etc. RT on shaking incubator, 900 rpm (o/n)
8. Wash 3 times with 1 mL B2 buffer, 10 min on rotating platform
9. Mount specimen in 80% glycerol/1x PBS
B1 buffer 1% BSA, 5% normal goat serum, 0.3% Tween PBST in PBS, 0.45 um filter sterilize, keep at 4˚C
B2 buffer 0.1% Tween PBST in PBS
PBST (phosphate buffered saline) 3% Tween 20