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PBMC Preparation for Flow Cytometry

**These protocols are meant to be modified with your experiment specifics in mind. 

ACK/Ammonium Lysis:

RBCs are disproportionately permeable to ammonium chloride and the uptake results in the accumulation of cytoplasmic ions inside the RBC and subsequent osmotic lysis through the uptake of H20 in physiological isotonic conditions. The PBMCs remain in ionic equilibrium with the isotonic buffer and are thus not lysed. Since the mechanism of action is dependent on having sufficient NH4Cl to lyse each RBC, the efficacy of this method would be affected if you had a sample with dramatically more or less RBCs as a side-effect of your experimental treatment. This can be easily circumvented by spinning down the blood and collecting the buffy coat to RBC-reduce the sample and proceed with “standard” ACK lysis.

Note that the Ammonium oxalate protocol is supposed to preserve morphology, number and function of all PBMCs better than other protocols but the strict control of osmolarity makes it more tedious. If you are interested, the detailed protocol can be found in J Lab Clin Med 1964;63:161-172.


  • MAKE SURE you use ddH20 to make your ACK/NH4Cl lysis buffer or the osmolarity will be insufficient to cause RBC lysis.

  • The anticoagulant used can affect the osmolarity, so try to use an anticoagulant like heparin (as opposed to sodium citrate).

  • Prewarm your lysis buffer to 37oC as opposed to using it cold- this allows the NH4Cl to enter the RBCs and lyse them with increased efficacy.

  • Neonatal RBCs are extremely resistant to osmotic stress/lysis and some drugs (i.e. ion chelating drugs, AZT, etc.) are known to interfere with this lysis procedure.

  • ENSURE that you pH your buffer properly. If the buffer pH is too far off, the ion pumps are affected and lysis does not occur.

  • *eBioscience ACK buffer purportedly lyses more than just the RBCs:

Ammonium Chloride Lysis Buffer

Water Lysis:

Water provides a potent hypotonic disequilibrium which would lyse all cells given enough time. The RBCs are quite structurally fragile compared to PBMCs and as such they lyse quite quickly while the PBMCs can survive the transient hypotonic shock. It is therefore critical that the water lysis is extremely brief (ideally 10-15 seconds).

The argument for using the water procedure over a more traditional ACK/ammonium chloride lysis approach is that the NH3 can enter the nucleus and change the nuclear pH. Some groups believe that the ammonium chloride approach can deleteriously affect the neutrophil count to a degree and/or affect the light scatter (F/SSC) signal for granulocytes.

The obvious benefit to this protocol is that it is incredibly easy and quick, with the downside that you have to be fast at “inactivating” the lysis by adding PBS/saline very quickly or you will lyse all of the cells. The first several times I did this it made me very nervous so my recommendation is to try this on a throw-away sample of mouse or human blood. This should be easy because getting a sample is very simple and there are no real reagents to be costly if it does not work. A simple validation by looking at FSC/SSC would act as an appropriate validation as would a hematological count.


  • Lyse RBCs via the addition of ddH20 (NOT RO, MilliQ or de-ionized water) for 15 seconds (<30 seconds is crucial).

  • Immediately dilute with an equal volume of 2x Ca/Mg free PBS or saline (1.8M NaCl)

  • Dilute in appropriate flow cytometry staining buffer (i.e. PBS + 2% BSA and 0.01% NaAzide for flow,  0.5% BSA for sorting with or without 1mM EDTA)

Fluorescent Trigger/Threshold of PBMCs:

RBCs and platelets are devoid of CD45 expression. By labeling CD45 on PBMCs and setting a fluorescent threshold on the cytometer, you can make the cytometer only record CD45-positive events. This method has the advantage of limited sample manipulation and being extremely easy with the drawback being that one of your fluorescent channels is taken up by CD45. Furthermore, if CD45 expression is very low (either naturally or as a result of your experimental system) and the threshold is not set carefully, you may accidentally remove these cells from analysis.


  • Label 106 PBMCs from anticoagulated whole blood with an appropriate CD45 antibody. I prefer short wavelength fluorophores as autofluorescence from monocytes make them appear a little “more” positive for CD45 than normal, which has no deleterious effect as we are trying to include them in the first place.

  • Incubate as per manufacturer’s protocol (i.e. 4oC for 10 mins). In many cases higher temperatures result in non-specific binding and ice requires longer incubation times. Be sure you follow the protocol precisely.

  • In the case of CD45 VioBlue (Miltenyi- link provided on Immunophenotyping section), you would start acquisition and slowly increase the V1 channel threshold/trigger until the RBC population just disappears.