After gating for CD4+ T cells using FlowJo, pre-processed data were considered for the analysis. All FlowSOM-based k-NN clustering was performed on the combined dataset to enable identification of small populations. For CD4+ TEMs, resulting nodes were meta-clustered with the indicated k-values (based on the elbow criterion) and annotated manually. FlowSOM k-NN clustering and two-dimensions UMAP projections were calculated using the CyTOF workflow package (v. 1.2)97 (link).
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