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Steps to Success with Multicolor Flow Cytometry

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Presentation on theme: "Steps to Success with Multicolor Flow Cytometry"— Presentation transcript:

1 Steps to Success with Multicolor Flow Cytometry
Holden T. Maecker

2 Outline Configure your instrument Characterize your instrument
Design your panel Optimize settings for your panel Run appropriate controls QC your data

3 Outline Configure your instrument These choices will determine:
Number and type of lasers Number of PMTs per laser Choice of filters and dichroic mirrors These choices will determine: What fluorochromes you can use effectively How well certain fluorochrome combinations will perform

4 How do we measure performance?
Resolution Sensitivity: D W2 W1 Stain Index = D / W Where D = difference between positive and negative peak medians, and W = 2 x rSD (robust standard deviation)

5 An Example: Green vs. Blue Lasers
Green laser more efficient for PE and PE tandems Green laser less efficient for FITC, PerCP and GFP CD127 PE 300 400 500 600 700 5 10 15 20 25 30 35 40 25 mW green laser (532 nm) 100 mW blue laser (488 nm) 25 mW blue laser (488 nm) PMT voltage Stain index

6 Second Example: Filters and Spillover

7 Outline Characterize your instrument This will allow you to:
Obtain minimum baseline PMT settings Track performance over time This will allow you to: Run the instrument where it is most sensitive Be alert to changes in the instrument that might affect performance

8 Automated baseline PMT voltage determination in Diva 6.0
Baseline PMTV is set by placing the dim bead MFI to equal 10X SDEN 460 V SDEN

9 Performance Tracking A variety of parameters can be tracked:
Linearity, CVs, laser alignment PMT voltages required to hit target values Data can be visualized in Levey-Jennings plots: 400 425 450 475 500 525 550 10/22/04 11/11/04 12/01/04 12/21/04 01/10/05 01/30/05 02/19/05 03/11/05 Time PMT Voltage FITC Channel (Blue laser)

10 Outline Design your panel This will allow you to:
Reserve brightest fluorochromes for dimmest markers and vice versa Avoid spillover from bright populations into detectors requiring high sensitivity Beware of tandem dye issues Titrate antibodies for best separation This will allow you to: Maintain resolution sensitivity where you most need it Avoid artifacts of tandem dye degradation

11 Various fluorochromes-stain index
Reagent Clone Filter Stain Index PE RPA-T4 585/40 356.3 Alexa 647 660/20 313.1 APC 279.2 PE-Cy7 780/60 278.5 PE-Cy5 695/40 222.1 PerCP-Cy5.5 Leu-3a 92.7 PE-Alexa 610 610/20 80.4 Alexa 488 530/30 75.4 FITC 68.9 PerCP 64.4 APC-Cy7 7801/60 42.2 Alexa 700 720/45 39.9 Pacific Blue 440/40 22.5 AmCyan 525/50 20.2

12 Spillover affects resolution sensitivity
Without CD45 AmCyan: With CD45 AmCyan: CD19 FITC Note that this is only an issue when the two markers (CD45 and CD19) are co-expressed on the same cell population.

13 Special requirements of tandem dyes
Compensation requirements for tandem dye conjugates can vary, even between two experiments with the same antibody Degrade with exposure to light, temperature, and fixation Stained cells are most vulnerable Solutions: Minimize exposure to above agents Use BD stabilizing fixative if a final fix is necessary Run experiment-specific compensation

14 False positives due to tandem degradation
With CD8 APC-Cy7 and CD4 PE-Cy7: Gating scheme CD8 APC-Cy7+ cells CD4 PE-Cy7+ cells False positives in APC channel reduced in absence of APC-Cy7 False positives in PE channel remain B. Without CD8 APC-Cy7:

15 New tandems can be more stable
APC-H7 as a replacement for APC-Cy7: Comparison of Sample Stability (in BD Stabilizing Fixative at RT) 250 200 CD4 APC-Cy7 150 CD8 APC-Cy7 % Spillover CD4 APC-H7 100 CD8 APC-H7 50 1 2 4 6 8 24 48 Hours of light exposure

16 Antibody titration basics
For most purposes, the main objective is to maximize signal:noise (pos/neg separation) This may occur at less than saturated staining This may or may not be the manufacturer’s recommended titer Titer is affected by: Staining volume (e.g., 100 mL) Number of cells (not critical up to ~5x106) Staining time and temperature (e.g., 30 min RT) Type of sample (whole blood, PBMC, etc.)

17 Antibody titration example

18 Outline Optimize settings for your panel This will allow you to:
Derive experiment-specific PMT settings Run compensation controls for each experiment This will allow you to: Use settings most appropriate for your panel Avoid gross errors of compensation

19 Experiment-specific setup for a new panel
Set voltages to achieve baseline target values Run single-stained CompBeads to see if each bead is at least 2x brighter in its primary detector vs. other detectors If not, increase voltage in the primary detector (beware: potential reagent problem) Run fully-stained cells and: Decrease voltages for any detectors where events are off-scale Increase voltages for any detectors where low-end resolution is poor (theoretically should not be necessary) Re-run single-stained CompBeads and calculate compensation Re-run fully-stained cells and repeat step 3 (if further changes made, re-run compensation) Save experiment-specific settings as target values Run samples

20 Experiment-specific setup for existing panel
Set voltages to achieve experiment-specific target channels Run single-stained CompBeads and calculate compensation Run samples

21 Outline Run appropriate controls This will allow you to:
Instrument setup controls (e.g., CompBeads) Gating controls (e.g., FMO) Biological controls (e.g., unstimulated samples, healthy donors) This will allow you to: Obtain consistent setup and compensation Gate problem markers reproducibly Make appropriate biological comparisons and conclusions

22 CompBeads as single-color controls
CompBeads provide a convenient way to create single-color compensation controls: Using the same Abs as in the experimental samples Creating a (usually) bright and uniform positive fluorescent peak Without using additional cells

23 Frequent compensation questions
Do I need to use the same antibody for compensation as I use in the experiment? Yes, for certain tandem dyes (e.g., PE-Cy7, APC-Cy7) Are capture beads better than cells for compensation? Usually, as long as the antibody binds to the bead and is as bright or brighter than stained cells Should compensation controls be treated the same as experimental samples (e.g., fixed and permeabilized)? Yes, although with optimal fix/perm protocols this may make little difference

24 Comparison of gating controls

25 Consider using lyophilized reagents
Lyophilization provides increased stability, even at room temperature or 37oC One batch of reagents can be used for an entire longitudinal study Pre-configured plates can avoid errors of reagent addition Complex experiments (multiple stimuli, multiple polychromatic staining cocktails) become easier Lyophilized cell controls can provide run-to-run standardization

26 Outline QC your data This will allow you to:
Visually inspect compensation Visually inspect gating Set sample acceptance criteria This will allow you to: Avoid classification errors and false conclusions due to improper compensation and/or gating, or sample artifacts

27 Visually inspect compensation
Create a template containing dot plots of each color combination in your experiment, then examine a fully stained sample for possible compensation problems Yikes!

28 Visually inspect gating
Check gating across all samples in the experiment Gates may need to be adjusted across donors and/or experimental runs; dynamic (e.g., snap-to) gates may help in some cases IFNg FITC IL-2 PE

29 Types of sample acceptance criteria
Minimum viability and recovery for cryopreserved PBMC Minimum number of events collected in an appropriate gate (e.g., lymphocytes) Minimum number of events within a region of interest, to calculate an accurate percentage

30 Outline Configure your instrument Characterize your instrument
Design your panel Optimize settings for your panel Run appropriate controls QC your data

31 A question for you to answer
How many colors can you combine and still have robust results? This depends on: -The experimental question -The instrument used -The markers to be combined

32 References Maecker, H. T., Frey, T., Nomura, L. E., and Trotter, J Selecting fluorochrome conjugates for maximum sensitivity. Cytometry A 62: 169. Maecker, H. T., and Trotter, J Flow cytometry controls, instrument setup, and the determination of positivity. Cytometry A 69: 1037. Roederer, M How many events is enough? Are you positive? Cytometry A 73: McLaughlin, B. E., N. Baumgarth, M. Bigos, M. Roederer, S. C. De Rosa, J. D. Altman, D. F. Nixon, J. Ottinger, C. Oxford, T. G. Evans, and D. M. Asmuth Nine-color flow cytometry for accurate measurement of T cell subsets and cytokine responses. Part I: Panel design by an empiric approach. Cytometry A 73:

33 Acknowledgements Laurel Nomura Margaret Inokuma Maria Suni
Maria Jaimes Smita Ghanekar Jack Dunne Skip Maino Joe Trotter Dennis Sasaki Marina Gever

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