Application protocol

Multicolor flow cytometric analysis of T cell subsets from mouse spleen


This application protocol describes the flow cytometric analysis of major T cell subsets after spleen dissociation from healthy C57BL/6 mice. Viable single cells from mouse spleens are easily obtained using the gentleMACS™ Technology. For downstream flow cytometric analysis of T cells, we have designed a validated multicolor flow cytometry panel, using our REAfinity™ Recombinant Antibodies and Viobility™ Fixable Dyes. In addition, we provide an optimized gating strategy for the analysis of naive, central memory, and effector memory T cells, as well as the expression of CD127 and KLRG1 on CD4+ and CD8+ T cells. 


The following is a listing of reagents, instruments, and consumables needed for each step of this protocol. These products are for research use only. 

For dissociation of mouse spleen

  • Phosphate-buffered saline (PBS), pH 7.2
  • PEB buffer: PBS, pH 7.2, 0.5% bovine serum albumin (BSA), and 2 mM EDTA.
  • gentleMACS Dissociator™ (# 130-093-235), gentleMACS Octo Dissociator (# 130-095-937), or gentleMACS Octo Dissociator with Heaters (# 130-096-427)
  • gentleMACS C Tubes (# 130-093-237, # 130-096-334)
  • MACS® SmartStrainers (70 µm) (# 130-098-462)
  • (Optional) Spleen Dissociation Kit, mouse (# 130-095-926)
  • (Optional) MACSmix™ Tube Rotator (# 130-090-753) in combination with an incubator at 37 °C
  • (Optional) ART® 1000 REACH™ pipet tips (Molecular BioProducts, Inc.) for removal of dissociated material from the closed C Tubes.

For flow cytometry staining and analysis

  • Phosphate-buffered saline (PBS), pH 7.2
  • PEB buffer: PBS, pH 7.2, 0.5% bovine serum albumin (BSA), and 2 mM EDTA.
  • Viobility™ 405/520 Fixable Dye (# 130-110-206, # 130-109-814)
  • CD4-VioBlue® (# 130-118-696)
  • CD62L-FITC (# 130-112-835)
  • CD127-PE (# 130-119-795)
  • CD3ε-PE-Vio® 615 (# 130-109-245)
  • CD44-PE-Vio 770 (# 130-110-119)
  • Anti-KLRG1-APC (# 130-117-089)
  • CD8a-APC-Vio 770 (# 130-120-806)
  • Deionized or distilled water
  • Flow cytometer, for example, MACSQuant® Analyzer 10 (# 130-096-343) or MACSQuant X (# 130-105-100) 
  • (Optional) MACSQuant Calibration Beads (# 130-093-607)
  • (Optional) MACS® Comp Bead Kit, anti-REA (# 130-104-693)
Matching products:


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This protocol includes detailed instructions for preparing necessary reagents and materials and then carrying out each step.


  • Always prepare reagents freshly.

Preparation of the PEB buffer

PEB buffer: Prepare a solution containing phosphate-buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin (BSA), and 2 mM EDTA by diluting MACS® BSA Stock Solution (# 130-091-376) 1:20 with autoMACS®. Rinsing Solution (# 130-091-222). Keep buffer cold (2–8 °C). Always use freshly prepared buffer. Do not use autoMACS. Running Buffer or MACSQuant® Running Buffer as they contain a small amount of sodium azide that could affect the results.

Reconstitution of the Viobility™ 405/520 Fixable Dye

Let the vials warm up to room temperature to avoid water condensation. Reconstitute one vial of lyophilized Viobility Fixable Dye by adding 100 μL anhydrous DMSO to the dye vial and mix until fully dissolved. Aliquot the solution and store at –20 °C under anhydrous conditions (desiccant) and protected from light for up to 1 month.


  • For details on the use of the gentleMACS™ Dissociators, refer to the gentleMACS Dissociator user manuals.
  • To obtain the results shown in this protocol one spleen per C Tube has been dissociated.
  1. Transfer mouse spleen into the gentleMACS C Tube containing the following amount of PEB buffer: 
    1–2 mouse spleens: 3 mL 
    3–4 mouse spleens: 6 mL 
    5–6 mouse spleens: 9 mL 
  2. Tightly close C Tube and attach it upside down onto the sleeve of the gentleMACS Dissociator. 
    Note: Close C Tube tightly beyond the first resistance.  
    Note: Ensure that the sample material is located in the area of the rotor/stator. 
  3. Choose and run one of the following gentleMACS Programs: 
    1–2 mouse spleens: m_spleen_01 
    3–6 mouse spleens: m_spleen_04 
  4. After termination of the program, detach C Tube from the gentleMACS Dissociator. 
  5. (Optional) Perform a short centrifugation step to collect the sample material at the bottom of the tube. 
  6. Resuspend sample and apply the cell suspension to a MACS SmartStrainer (70 μm), placed on a 15 mL tube (1–2 mouse spleens per C Tube) or to a 50 mL tube (3–6 mouse spleens per C Tube). 
    Note: Moisten MACS SmartStrainer with 2 mL buffer before use. 
    Note: Dissociated tissue can be removed from the closed C Tube by pipetting through the septum-sealed opening in the center of the cap of the C Tube. Use ART® 1000 REACH™ 1000 μL pipette tips. 
  7. Wash the filter with 5 mL of PEB buffer. 
  8. Discard the filter and centrifuge cell suspension at 300×g for 10 minutes at room temperature. Aspirate supernatant completely. 
  9. Resuspend cells in PEB buffer to an appropriate volume and proceed to flow cytometry staining. 

Configuration of the panel

LaserAntibody specificityFluorochromeClone
 Viobility 405/520 Fixable Dye 
CD3εPE-Vio® 615REA606
CD44PE-Vio 770REA644
CD8aAPC-Vio 770REA601

Labeling of cells with Viobility™ 405/520 Fixable Dye


  • Volumes given below are for up to 10⁷ nucleated cells. When working with fewer than 10⁷ cells, use the same volumes as indicated. When working with higher cell numbers, scale up all reagent volumes and total volumes accordingly (e.g. for 2×10⁷ nucleated cells, use twice the volume of all indicated reagent volumes and total volumes).
  1. Determine cell number.
  2. Wash cells in 1 mL of 1× PBS and centrifuge at 300×g for 10 minutes. Aspirate supernatant completely.
  3. Resuspend cells in 100 μL of 1× PBS.
  4. Add 1 µL of Viobility™ 405/520 Fixable Dye.
  5. Mix well and incubate for 15 minutes in the dark at room temperature.
    Note: Higher temperatures and/or longer incubation times may lead to nonspecific cell labeling. Working on ice requires increased incubation times.
  6. Wash cells by adding 1 mL PEB buffer and centrifuge at 300×g for 10 minutes. Aspirate supernatant completely.
  7. (Optional) Repeat step 6.
  8. Proceed with surface staining.

Surface staining


  • To obtain the results shown in this protocol a total of 1×10⁶ splenocytes has been stained in a total volume of 100 µL.
  1. Determine cell number.
  2. Centrifuge cell suspension at 300×g for 10 minutes. Aspirate supernatant completely.
  3. Prepare a master mix with all fluorochrome-conjugated antibodies according to the respective data sheets.
  4. Add master mix to the cell suspension.
  5. Mix well and incubate for 10 minutes in the dark in the refrigerator (2−8 °C).
    Note: Higher temperatures and/or longer incubation times may lead to non-specific cell labeling. Working on ice requires increased incubation times.
  6. Wash cells by adding 1 mL of PEB buffer and centrifuge at 300×g for 10 minutes. Aspirate supernatant completely.
  7. Resuspend cells in an appropriate volume of PEB buffer and proceed to flow cytometry analysis.


  • Prior acquisition of samples in a flow cytometer, e.g., the MACSQuant® Analyzer 10, make sure lasers are properly calibrated (by using, e.g., the MACSQuant Calibration Beads), and compensation of the spillover of fluorochrome emissions has been established in advance using cells or the MACS® Comp Bead Kit, anti-REA. Prior acquisition adjust also forward scatter (FSC)/side scatter (SSC) parameters to properly locate all leukocyte populations in the plots.
  1. Exclude doublets by using the FSC-H/FSC-A parameters.
  2. Use gated single cells to exclude erythrocytes and debris using the SSC/FSC parameters.
  3. Use the SSC/FSC gate to exclude dead cells from the analysis using the Viobility Dye/FSC.
  4. Use gated Viobility™ Dye–negative (viable) cells to identify regulatory T cells.
View details

Gating strategy showing the analysis of T cell subsets from mouse spleen. Splenocytes from C57BL/6 mice were stained using the previously described antibody panel to analyze major T cell subsets. Frequencies of naive, central memory (CM), and effector memory (EM) T cells were analyzed for CD4 and CD8 T cells, respectively, based on the expression of the adhesion molecules CD44 and CD62L. Naive T cells express high levels of the CD62L molecule and low or negative CD44 expression. Both, CM and EM populations express CD44, but CM T cells express also CD62L, whereas expression of CD62L is absent in EM T cells. The analysis of the IL7-R alpha chain (CD127) and KLRG1 is included in this panel to allow the study of T cell responses during infection. During the course of an infection the levels of KLRG1 increase, especially on CD8 T cells.

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