Mass Cytometry (CyTOF) profiling of baseline influenza virus-reactive T-cells in a Controlled Human Influenza Challenge (CHIM) study

This dataset contains the raw mass cytometry (CyTOF) files associated with the publication: "Innate antiviral readiness drives the expansion of protective T stem cell memory against influenza."

To determine the clinical relevance of T stem cell-like memory (TSCM) cells, this study analyzed an independent Controlled Human Influenza Challenge (CHIM) cohort (n = 9). This validation cohort was used to investigate the role of memory CD8+ T-cell subsets in host defense, in which baseline memory CD8 T-cell frequencies were evaluated as predictors of rapid viral load clearance, distinct from antibody-mediated symptom mitigation.

Experimental Design The dataset includes paired .fcs files for 9 individuals at the pre-infection baseline timepoint. Each subject has files for two conditions:

• Unstimulated Controls: Matched samples processed in parallel without peptide stimulation.

• Antigen Stimulation: Thawed PBMCs stimulated for 12-16 hours with a comprehensive peptide pool library spanning the entire proteome of influenza A/California/07/2009, consisting of 483 20-mers and 24 9-mers.

Methodology

• Panel: Cells were stained with a 36-marker metal-labeled antibody panel designed to distinguish T-cell memory subsets (including TSCM) and intracellular cytokine production. The workflow included surface labeling, fixation (Maxpar Fix I), permeabilization (Maxpar Perm Buffer), and intracellular staining.

• Acquisition: Data were acquired on a Fluidigm Helios mass cytometer.

• Analysis Software: Data were analyzed initially using Cytosplore and FlowJo.