multiple flow cytometry dot plots of different cell populations in immunophenotyping experiment

This section provides educational resources and tools for immunophenotyping by flow cytometry. These resources include a panel design tool, review articles, application notes, protocols, fluorophore guides and more.

Immunophenotyping features

Review article

European Journal of Immunology Cover Volume 47 Issue 10

Guidelines for the use of flow cytometry and cell sorting in immunological studies

This special edition of the European Journal of Immunology is a comprehensive resource prepared by flow cytometry and immunology research experts from around the world. The Flow Cytometry Guidelines not only highlight the latest trends and best practices in basic and advanced flow cytometry but also re‐enforce optimal sample preparation, as well as data analysis, enabling the correct use of state of the art flow cytometry for all involved in immunological research

Panel design tool

Screen view of the Thermo Fisher Scientific flow cytometry panel design tool with viability dye and 2 antibody options for the violet and the blue lasers

Flow Cytometry Panel Builder

This online tool guides you through flow cytometry panel design, providing a simplified, customizable experience to fit your flow cytometry panel design needs.


Immunophenotyping subtopics


Immunophenotyping learning resources

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Type Title Categories
Application note (2017) Validated 10-color T cell panel using the Attune NxT Flow Cytometer antibodies, Attune/Attune NxT Flow Cytometer, flow cytometry, immunology, immunophenotyping, fluorescent dyes, multicolor flow cytometry
Application note (2017)  Detection of platelets in whole blood using the Attune NxT Flow Cytometer  Attune NxT, flow cytometer, platelets, immunophenotyping, no-wash, no-lyse
Application note (2015) Attune NxT Flow Cytometer for 6-color immunophenotyping analysis of stained human whole blood using a no-lyse, no-wash protocol, with no compensation Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Detection of murine regulatory T cells on the Attune NxT Flow Cytometer Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Multiparameter analysis of murine regulatory T cells and dendritic cells with the Attune NxT Flow Cytometer Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Ten-parameter immunophenotyping of human lysed whole blood with the Attune NxT Flow Cytometer allows identification of multiple T cell subsets and myeloid cells Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015)  13-parameter immunophenotyping of human lysed whole blood with the Attune NxT Flow Cytometer allows for the identification of B cells, NK cells, multiple T cell subsets and myeloid cells  Alexa Fluor, antibodies, Attune NxT, compensation, flow cytometer, fluorescent dyes, immunophenotyping, multicolor flow cytometry, nanocrystals, Qdot
BioProbes articles (Issues 50– present day) BioProbes Journal of Cell Biology Application cell analysis, flow cytometry, imaging microscopy, immunoassays, antibodies, protein detection and quantification
Blog post Super Bright conjugates for flow cytometry antibodies, Attune NxT, flow cytometry, immunophenotyping, multicolor flow cytometry, Super Bright
Fluorophore Pacific Blue dye antibody conjugates, flow cytometry, immunophenotyping, violet laser
Fluorophore Pacific Green dye antibody conjugates, flow cytometry, immunophenotyping, violet laser
Fluorophore Pacific Orange dye antibody conjugates, flow cytometry, immunophenotyping, violet laser
Fluorophore Super Bright 436 dye antibody conjugates, flow cytometry, immunophenotyping, tandem polymer dyes, violet laser
Fluorophore Super Bright 600 dye antibody conjugates, flow cytometry, immunophenotyping, tandem polymer dyes, violet laser
Fluorophore Super Bright 645 dye antibody conjugates, flow cytometry, immunophenotyping, tandem polymer dyes, violet laser
Fluorophore Super Bright 702 dye antibody conjugates, flow cytometry, immunophenotyping, tandem polymer dyes, violet laser
Fluorophore Allophycocyanin (APC) antibody conjugates, flow cytometry, immunophenotyping, phycobiliproteins, tandem dyes
Fluorophore R-phycoerythrin (R-PE) antibody conjugates, flow cytometry, immunophenotyping, phycobiliproteins, tandem dyes
Fluorophore Cyan fluorescent protein (CFP) flow cytometry, fluorescent proteins
Fluorophore Green fluorescent protein (GFP) flow cytometry, fluorescent proteins
Fluorophore Red fluorescent protein (RFP) flow cytometry, fluorescent proteins
Fluorophore Fluorophore selection guide antibody conjugates, flow cytometry, immunophenotyping
Guided learning T cell stimulation and proliferation eLearning course antibodies, cell proliferation, cell stimulation, flow cytometry, immunoassays, immunology, immunophenotyping, T cells
Guided learning Antibody validation eLearning course antibodies
Molecular Probes Handbook Phycobiliproteins—Section 6.4 antibody labeling, multicolor flow cytometry, tandem conjugates
Molecular Probes Handbook Using the Fluorescence SpectraViewer—Note 23.1 flow cytometry, fluorescence, fluorescence microscopy/fluorescence imaging, fluorescent dyes, fluorescent proteins
Molecular Probes Handbook Zenon Technology: Versatile reagents for immunolabeling—Section 7.3 antibody labeling, flow cytometry, fluorescence microscopy/fluorescence imaging, secondary detection, Zenon
Immunology information Foxp3 overview flow cytometry, Foxp3,intracellular staining
Protocols Cell preparation for flow cytometry protocols (Invitrogen eBioscience reagents) flow cytometry, sample preparation
Protocols Red blood cell lysis protocols using eBioscience lysis buffers (Invitrogen eBioscience reagents) flow cytometry, sample preparation
Protocols Staining cell surface targets for flow cytometry (Invitrogen eBioscience reagents) extracellular staining, flow cytometry, immunophenotyping
Protocols Staining intracellular antigens for flow cytometry (Invitrogen eBioscience reagents) flow cytometry, immunophenotyping, intracellular staining
Protocols  Super Bright staining buffer protocol  antibody conjugates, flow cytometry, immunophenotyping
Scientific poster (2018)  Modular, defined assembly of antibody-based constructs using click chemistry  Alexa Fluor, antibody labeling, Attune/Attune NxT, CellInsight, drug discovery, drug research, high content analysis (HCA), SiteClick, spheroids
Scientific poster (2018)  Prospective cytometric study evaluating the alkaline phosphatase activity as a potential functional biomarker of primitive malignant cells in acute leukemia  antibodies, Attune/Attune NxT, cancer, cell function, flow cytometry, immunophenotyping, stem cell research
Scientific Poster (2017)  T-lymphocyte immunophenotyping: 14-color flow cytometry panel design using the Attune NxT Flow Cytometer and Super Bright fluorescent dyes  antibodies, Attune NxT, fluorescent dyes, immunophenotyping, multicolor flow cytometry, particles, Super Bright
Scientific Poster (2015)  A no lyse, no-wash approach to characterizing phagocyte phenotype and function in whole human blood on the Attune NxT Flow Cytometer  Attune NxT, cell cycle, flow cytometer, flow cytometry assays, immunophenotyping, no lyse, phagocytosis, whole blood
Scientific poster (2014) Copper-safe Click-iT Plus EdU proliferation assay: Improved compatibility with simultaneous phycobiliprotein and fluorescent protein detection cell proliferation, Click-iT, flow cytometry, immunophenotyping
Scientific poster (2013)  Improved click chemistry demonstrating EdU cell proliferation with GFP-expressing cells and R-PE-based immunophenotyping  Alexa Fluor, cell cycle, cell proliferation, Click-iT, flow cytometry assays, fluorescent dyes, fluorescent proteins, immunophenotyping
Scientific poster (2010)  Proliferative and phenotypic characterization of human mesenchymal stem cells by flow cytometry and imaging Alexa Fluor, cell proliferation, cells, Click-iT, flow cytometry, fluorescence microscopy/fluorescence imaging, fluorescent dyes, immunofluorescence (IF), immunophenotyping, stem cell research, violet laser-excited reagents
Scientific poster (2009)  A comparative study of 25 different CD4 conjugates  Alexa Fluor, antibodies, fluorescent dyes, immunophenotyping, multicolor flow cytometry, nanocrystals, Qdot
Scientific poster (2009)  A novel xeno-free and serum-free culture medium for the expansion of human mesenchymal stem cells  cell culture, cell expansion, flow cytometry, fluorescent dyes, gene expression, immunophenotyping, stem cell research
Scientific poster (2009)  A simple, fast and quantitative single-step dead-cell indicator for flow cytometry  apoptosis, fluorescent dyes, multicolor flow cytometry, nucleic acid quantitation, viability
Scientific poster (2009)  Dead cell stains in flow cytometry: A comprehensive analysis  apoptosis, cells, flow cytometry, fluorescent dyes, immunophenotyping, viability
Scientific poster (2009)  Proliferative and phenotypic characterization of human mesenchymal stem cells by flow cytometry  Alexa Fluor, cell proliferation, cells, Click-iT, flow cytometry, fluorescent dyes, fluorescent proteins, immunophenotyping, nucleic acid quantitation, stem cell research, violet laser-excited reagents
Scientific poster (2008)  Zenon labeling technology facilitates detection of intra-cellular phosphoprotein determinants  Alexa Fluor, antibodies, cell signaling, cells, flow cytometry, fluorescent dyes, protein labeling, rare cell detection, Zenon
Selection guide Antibody fixation considerations sample preparation
Selection guide Human antibody cross reactivity chart antibody cross-reactivity, flow cytometry
Selection guide Mouse antibody cross reactivity chart antibody cross-reactivity, flow cytometry
Selection guide Cytokine bioassays guide cytokines, flow cytometry, immunophenotyping, intracellular staining
Selection guide Intracellular staining guide (for mouse & human cytokines and non-cytokine proteins) cytokines, flow cytometry, intracellular staining
Selection guide Human CD & other cellular antigens flow cytometry, immunology, immunophenotyping, extracellular staining
Selection guide Intracellular staining buffer selection guide flow cytometry, immunophenotyping, intracellular staining
Selection guide Mouse CD & other cellular antigens flow cytometry, immunology, immunophenotyping, extracellular staining
Selection guide Phospho flow cytometry antibody clone buffer selection guide flow cytometry, immunophenotyping, intracellular staining, phosphoflow cytometry
CYToMORE lecture video (2016) Assessing immunological aging using flow cytometry 
Presented by Victor Appay, Faculté de Médecine Pierre et Marie Curie, Pitié-Salpêtrière, France
flow cytometry, immunology, immunophenotyping
CYToMORE lecture video (2016) Cytometric analysis of cytokines and transcription factors 
Presented by Hyun-Dong Chang, Deutsches Rheuma-Forschungszentrum, Berlin, Germany
cell signaling, flow cytometry, immunophenotyping
CYToMORE lecture video (2016) Heterogeneity of tumour-infiltrating leukocytes: implications for adoptive cell transfer immunotherapy 
Presented by Enrico Lugli, Humanitas Clinical and Research Center, Italy
flow cytometry, immunology, immunophenotyping
CYToMORE lecture video (2016) Mass cytometry in the phenomics era: an essential tool for gene/function studies 
Presented by Herve Luche, Centre d’Immunophénomique - CIPHE, France
immunology, immunophenotyping, mass cytometry
How-to video Tutorial: Labeling a purified antibody 
Educational video on how to label your next antibody for imaging or fluorescence. Walk through the tutorial as Molecular Probes scientists demonstrate the protocol—including all the tips and tricks you'll want to know about for your next antibody labeling experiment. The video features Judie showing Curtis, a chemistry graduate student, how to label his monoclonal antibodies while saving time and maximizing yield.
antibodies, antibody labeling, flow cytometry, fluorescence microscopy/fluorescence imaging, fluorescent dyes
How-to video How to site specifically label your antibody using SiteClick technology 
This video explains how to easily and site specifically label an antibody using an enzymatic and Click chemistry approach. This method can be applied to any intact IgG antibody and requires no antibody engineering or complex methodology. Unlike classic antibody conjugation techniques this breakthrough SiteClick technology allows for antibody conjugation with complete confidence that the label will not directly interfere with the antibody binding domain.
antibodies, antibody labeling, flow cytometry, fluorescence microscopy/fluorescence imaging, fluorescent dyes, Qdot, western detection
Webinar A practical approach to antibody labeling 
The growing number of fluorophores available makes labeling your own antibodies a tempting proposition. But with many antibody labeling solutions available, selecting the best option can be a daunting task. In this webinar we will:
  • Provide an overview of our antibody labeling kits
  • Offer guidance on which methods are ideal for specific applications and experiments
  • Provide tips and tricks to optimize your labeling protocol
antibodies, antibody labeling, flow cytometry, fluorescence microscopy/fluorescence imaging, immunofluorescence (IF)
Webinar Learn to choose the right fluorophore when designing experiments 
The choice of fluorophore is one of the first important decisions to make in developing an experiment. Fluorophores are compounds that emit light at a specific wavelength when they have been excited at another, lower wavelength. In this webinar we will explore:
  • How to choose the best organic dye for an assay
  • Quantum dots and how they compare to other dyes
  • When to use a phycobiliprotein like R-PE or APC
  • When to use fluorescent proteins like GFP
  • How to choose a suitable dye to match your instrument
In addition, we will review the basic characteristics, strengths, and weaknesses of the various fluorophores to help you choose and develop the best assay for your needs.
antibodies, antibody labeling, flow cytometry, fluorescence microscopy/fluorescence imaging, fluorescent dyes, fluorescent proteins

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.