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2 INSERM U1223, Paris, France
3 Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
4 Flow Cytometry Platfrom, Cytometry and Biomarkers UtechS, Center for Translational Science, Pasteur Institute, Paris, France
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Related Experiment Video

Updated: Jan 19, 2026

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High-Dimensional Immunophenotyping with Fluorescence-Based Cytometry: A Practical Guidebook.

Florian Mair1, Aaron J Tyznik2

  • 1Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. fmair@fredhutch.org.

Methods in Molecular Biology (Clifton, N.J.)
|September 16, 2019
PubMed
Summary
This summary is machine-generated.

This guide offers practical strategies for designing and executing complex fluorescence-based immunophenotyping panels. It addresses common challenges in quality control and data analysis for high-dimensional flow cytometry.

Keywords:
CompensationFlow cytometryFluorescenceHigh-dimensionalImmunologyPanel designPolychromaticSSMSpillover spreadingStaining

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Area of Science:

  • Immunology
  • Biotechnology
  • Cell Biology

Background:

  • High-dimensional single-cell immunophenotyping utilizes advanced technologies like mass cytometry, single-cell RNA sequencing, and flow cytometry.
  • Fluorescence-based flow cytometry is the most prevalent method, with modern instruments measuring up to 30 parameters.
  • These techniques provide profound insights into the intricate nature of the immune system.

Purpose of the Study:

  • To provide a practical guidebook for designing and executing complex fluorescence-based immunophenotyping panels.
  • To address common misconceptions and potential pitfalls in panel design and execution.
  • To discuss challenges related to quality control and data analysis in high-dimensional flow cytometry.

Main Methods:

  • The study focuses on fluorescence-based immunophenotyping panels.
  • It details practical aspects of panel design and execution.
  • It covers quality control and data analysis strategies for complex datasets.

Main Results:

  • The guidebook addresses common misconceptions and caveats in fluorescence-based immunophenotyping.
  • It highlights challenges in quality control and data analysis for high-dimensional datasets.
  • Practical strategies for successful panel design and execution are provided.

Conclusions:

  • Effective design and execution of complex immunophenotyping panels are crucial for accurate immune system analysis.
  • Addressing common challenges in quality control and data analysis enhances the reliability of flow cytometry data.
  • This guidebook serves as a valuable resource for researchers utilizing high-dimensional flow cytometry.