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Cell Cycle Analysis Using Propidium Iodide Staining with GFP Detection   

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Infecting mammalian cells with a GFP construct to overexpress or knockdown target genes is one of the most commonly used methods to study and manipulate gene expression. To determine the target gene function on the cell cycle, analyzing the cell cycle (propidium iodide, PI staining) of GFP positive cells vs GFP negative cells is needed. Usually simple fixation of cells with 70% EtOH for PI staining tends to quench GFP signal; paraformaldehyde (PFA) fixation before ETOH fixation could help to sustain the GFP signal.

Keywords: Cell cycle, GFP, FACS, Propidium iodide

Materials and Reagents

  1. Phosphate buffered saline (PBS)
  2. Glucose (Sigma-Aldrich, catalog number: G8270 )
  3. Paraformaldehyde (Electron Microscopy Sciences, catalog number: 15170 )
  4. 70% EtOH
  5. Hepes (Sigma-Aldrich, catalog number: H3375 )
  6. NP-40 (MBL International, catalog number: JM-2111-100 )
  7. BSA (Sigma-Aldrich, catalog number: A3803 )
  8. RNase A (Sigma-Aldrich, catalog number: R4642 )
  9. Fix solution (see Recipes)
  10. Wash solution (see Recipes)


  1. Centrifuges (Beckman Falcon, TLS-55 )
  2. 15 ml polypropylene falcon tubes (BD Biosciences, Falcon®, catalog number: 352097 )
  3. FACS machine


  1. Trypsinize and harvest cells, suspend in 10 ml PBS into 15 ml polypropylene falcon tubes.
  2. Pellet cells at 1,500 rpm, 3 min, aspirate supernatant.
  3. Wash cells 1x in 5 ml PBS.
  4. Pellet cells at 1,500 rpm, 3 min, aspirate supernatant.
  5. Thoroughly resuspend cells 1 ml fix solution.
  6. Incubate 10 min on ice.
  7. Add PBS up to 14-15 ml.
  8. Pellet cells at 1,500 rpm, 3 min, aspirate supernatant.
  9. Wash cells 1x in 5 ml PBS.
  10. Resuspend cells in 0.5 ml 1x PBS. Vortex tube gently and add 4.5 ml ice cold 70% EtOH dropwise over 30 sec to 1 min. Incubate on ice > 1 h.
  11. Pellet cells at 1,500 rpm, 3 min, aspirate supernatant.
  12. Wash cells 1x in wash solution.
  13. Pellet cells at 1,500 rpm, 3 min, aspirate supernatant.
  14. Resuspend cells in 500 μl of PBS containing 10 μg ml-1 RNase A and 20 μg ml-1 PI, transfer to FACS tubes and incubate at room temperature in the dark for 30 min.
  15. FACS immediately or store at 4 °C until FACS analysis.


  1. Fix solution
    1x PBS
    2% Glucose
    3% Paraformaldehyde
  2. Wash solution
    1x PBS
    20 mM Hepes
    0.25% NP-40
    0.1% BSA


This work was supported by the California Institute of Regenerative Medicine, Grant RL1-00100.


  1. Zhu, H., Coppinger, J. A., Jang, C. Y., Yates, J. R., 3rd and Fang, G. (2008). FAM29A promotes microtubule amplification via recruitment of the NEDD1-gamma-tubulin complex to the mitotic spindle. J Cell Biol 183(5): 835-848.
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Copyright: © 2012 The Authors; exclusive licensee Bio-protocol LLC.
How to cite: Zhu, H. (2012). Cell Cycle Analysis Using Propidium Iodide Staining with GFP Detection. Bio-101: e199. DOI: 10.21769/BioProtoc.199.

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Wu Sian
Can I use GFP-antibody to improve green florescence and then use PI stain to detect cell cycle? Any protocol can I follow?
9/7/2017 5:55:43 PM Reply
Hui Zhu
Stanford University

I have used GFP antibody in Immunofluorescence staining. For FACS, I have never tried. If GFP+ % is fairly high, you don't need to add antibody. If GFP+ % is very low, adding antibody may not help.

9/7/2017 7:07:44 PM

I have problems to detect the florescence of PI and GFP together, as their emission is very similar. Any suggestions?
6/8/2012 7:06:16 PM Reply
hui zhu
stanford universtiy

PI is much more broader which fluoresces everywhere from yellow to far-red.
You need to do compensation when go with GFP. You can use 7-AAD in place of
PI, which is more tighter.

6/10/2012 2:39:51 PM

Why glucose here?
2/14/2012 12:21:55 PM Reply
hui zhu
stanford universtiy

Paraformaldehyde is godd to penetrate cells. The disadvantage is that paraformaldehyde Only partially destroys osmotic properties of membranes. Osmolarity must be carefully adjusted by glucose or sucrose.

2/22/2012 2:48:32 AM

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