BODIPY 493/503

Protocol for BODIPY 493/503 staining with flow cytometry ^[1]
1. Grow cells under culture conditions relevant for the study. (For example, 50,000 A498 cells in 35 mm well.)
Note: Overnight incubation of cells with 30 μM oleic acid can serve as a positive control for increased neutral lipid content, as oleic acid is a potent inducer of triglyceride synthesis and storage. Fatty acid free BSA serves as a control.
2. At the time-point of interest, prepare 2 μM BODIPY 493/503 staining solution in PBS.
3. Wash cells with a quick rinse using 3 ml PBS to remove media/serum.
4. Incubate on BODIPY 493/503 staining solution in the dark for 15 min at 37 °C. Include an unstained control for flow cytometry.
5. Wash cells with a quick rinse using 3 ml PBS to remove staining solution.
6. Trypsinize cells to generate a single cell suspension. For the A498 cell line used in this protocol, cells were incubated with Trypsin-EDTA (0.25%) for 5 min at 37 °C.
7. Add 5 ml of PBS and transfer cell suspension to a 15 ml conical tube.
8. Pellet cells at 250×g, 5 min, 4 °C.
9. Aspirate supernatant, wash the cell pellet with a quick rinse using 3 ml PBS, and pellet cells at 250 ×g, 5 min, 4 °C.
10. Carefully aspirate the supernatant and resuspend cells in 300 μl 1x flow cytometry buffer.
11. Pass cell suspension through a 35 μm filter into a FACS tube.
12. Perform flow cytometry. Obtain a minimum of 10,000 events per condition.
13. The investigator can analyze data as mean fluorescence or display the data as a histogram.

Protocol for BODIPY 493/503 staining with microscopy ^[1]
1. Autoclave coverslips in a glass bottle.
2. In the tissue culture hood, place coverslips into 35 mm cell culture dishes.
3. Prepare 2 mg/ml collagen solution in PBS.
4. Treat the coverslips with collagen to promote cell adherence. Add 3 ml collagen solution to culture dishes and incubate at 37 °C for 30 min.
Note: Use forceps to ensure that coverslips are flush with the bottom of the culture dish, eliminating any air bubbles that may be under the cover slips.
5. Aspirate the collagen solution.
6. Wash with PBS.
7. Add PBS to culture dishes and place under UV light in the culture hood to sterilize.
8. Plate cells into culture dishes containing the coverslips. The optimal cell number should be determined to achieve confluence of 30-50% at the time of staining to permit proper imaging. For A498 cells used in this protocol, 100,000 cells were plated in 35 mm wells to permit staining at 48 h post plating.
9. Incubate under the culture conditions relevant to your experiment.
a. For this protocol, A498 cells were incubated in DMEM (high glucose, L-glutamine, sodium pyruvate) supplemented with 10% FBS at 37 °C.
b. Overnight incubation of cells with 30 μM oleic acid with BSA can serve as a positive control for increased neutral lipid content, as oleic acid is a potent inducer of triglyceride synthesis and storage. Fatty acid free BSA serves as a control.
10. At the time-point of interest, prepare 2 μM BODIPY 493/503 staining solution in PBS.
a. For this protocol, A498 cells were stained 48 h after plating, after an overnight incubation with BSA or BSA + oleic acid.
11. Wash cells with 3 ml PBS.
12. Incubate on 3 ml staining solution for 15 min at 37 °C.
Note: From this point, protect samples from light as much as possible.
13. Wash twice in 3 ml PBS.
14. Fix cells in 3 ml 4% PFA for 30 min at room temperature.
15. Remove 4% PFA.
16. Wash samples 3 x 5 min in PBS.
17. Use forceps to mount cover slips onto glass slides.
Use forceps to pick up cover slips and place onto the drop of mounting solution, ensuring that the side that side with cells is placed face down onto the glass slides.
18. Allow the mounting solution to cure overnight at room temperature.
19. Immediately image cells.
BODIPY 493/503 photobleaches rapidly. Including 200 ng/ml of BODIPY 493/503 in the medium during imaging can minimize this problem. Additionally, using the stable Hoechst staining in the blue channel to find, focus, and center fields before imaging BODIPY 493/503 in the green channel diminishes photobleaching ^[2] .
2 μM BODIPY staining solution：
a. Prepare 5 mM BODIPY stock solution
Dissolve 1.3 mg BODIPY in 1 ml DMSO and can be stored at -20 °C, protect from light.
b. 2 μM BODIPY staining solution can be prepared by diluting stock solution 1:2,500 in PBS.

This protocol only provides a guideline, and should be modified according to your specific needs

References:
[1]. Qiu, B. and Simon, M. C. (2016). BODIPY 493/503 Staining of Neutral Lipid Droplets for Microscopy and Quantification by Flow Cytometry. Bio-protocol 6(17): e1912. DOI: 10.21769/BioProtoc.1912.
[2]. Listenberger, L.L., Studer, A.M., Brown, D.A., and Wolins, N.E. 2016. Fluorescent detection of lipid droplets and associated proteins. Curr. Protoc. Cell Biol. 71:4.31.1-4.31.14. doi: 10.1002/cpcb.7