Immune cell subset frequencies by mass cytometry across 14 malaria, schistosomiasis and hookworm vaccine and controlled human infection trials

This dataset contains the frequencies of 20 immune cell subsets in peripheral blood, measured by mass cytometry (CyTOF) in 669 samples from 14 clinical trials in malaria, schistosomiasis and hookworm. The trials include controlled human infection studies and vaccine trials conducted in the Netherlands, Germany, Gabon, Equatorial Guinea and Tanzania. This makes it possible to compare immune profiles of participants from non-endemic and endemic regions. Highlights include GA2, the first malaria challenge trial using genetically attenuated sporozoites; CoHSI1, the first Schistosoma mansoni challenge trial in Europe; and CHHIL, the first hookworm challenge trial in the Netherlands. Cell subsets were identified in six separate self-organising map (SOM) analyses, which were merged using mutual nearest neighbours (MNN) batch correction and joint hierarchical metaclustering. Each subset is therefore comparable across all studies. Values are percentages of CD45+ cells. All underlying clinical and experimental data are FAIR and available through controlled access via the LUCID FAIR Data Point (https://fdp.lucid.lumc.nl). This open dataset lowers the barrier to reuse: it can be downloaded without a data access request, and explored interactively in the Cell Subset Explorer at https://data.hypovax.org. Data were harmonised and exported with the open-source R package beFAIR (https://doi.org/10.5281/zenodo.23018363). Files: cell_subsets_open.csv (data), data_dictionary.csv (variable descriptions), README.md (full methods, study overview and consortium information).