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Visualization and Quantification of High-Dimensional Cytometry Data using Cytofast and the Upstream Clustering Methods FlowSOM and Cytosplore
- Source :
- Journal of Visualized Experiments. JOURNAL OF VISUALIZED EXPERIMENTS, ISSUE=154;TITLE=Journal of Visualized Experiments
- Publication Year :
- 2019
-
Abstract
- The complexity of data generated by mass cytometry has necessitated new tools to rapidly visualize analytic outcomes. Clustering methods like Cytosplore or FlowSOM are used for the visualization and identification of cell clusters. For downstream analysis, a newly developed R package, Cytofast, can generate a rapid visualization of results from clustering methods. Cytofast takes into account the phenotypic characterization of cell clusters, calculates the cell cluster abundance, then quantitatively compares groups. This protocol explains the applications of Cytofast to the use of mass cytometry data based on modulation of the immune system in the tumor microenvironment (i.e., the natural killer [NK] cell response) upon tumor challenge followed by immunotherapy (PD-L1 blockade). Demonstration of the usefulness of Cytofast with FlowSOM and Cytosplore is shown. Cytofast rapidly generates visual representations of group-related immune cell clusters and correlations with immune system composition. Differences are observed in the clustering analysis, but separation between groups are visible with both clustering methods. Cytofast visually shows the patterns induced by PD-L1 treatment that include a higher abundance of activated NK cell subsets, expressing a higher intensity of activation markers (i.e., CD54 or CD11c).
- Subjects :
- 0301 basic medicine
Computer science
medicine.medical_treatment
General Chemical Engineering
high-dimensional analysis
Cell
02 engineering and technology
Computational biology
Lymphocyte Activation
visualization tool
B7-H1 Antigen
General Biochemistry, Genetics and Molecular Biology
Issue 154
Mice
03 medical and health sciences
Single-cell analysis
Tumor Microenvironment
medicine
Animals
Cluster Analysis
single-cell analysis
Mass cytometry
Cluster analysis
Immunology and Infection
Tumor microenvironment
General Immunology and Microbiology
General Neuroscience
R package
Immunotherapy
data mining
flow and mass cytometry analysis
Flow Cytometry
021001 nanoscience & nanotechnology
Visualization
Killer Cells, Natural
Mice, Inbred C57BL
030104 developmental biology
medicine.anatomical_structure
0210 nano-technology
Cytometry
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Journal of Visualized Experiments. JOURNAL OF VISUALIZED EXPERIMENTS, ISSUE=154;TITLE=Journal of Visualized Experiments
- Accession number :
- edsair.doi.dedup.....478c184320acdce40e6511fe77c4f944