Acute COVID-19 cohort - peripheral blood mononuclear cells across disease severity and time

COVID_annotation_07062023

Manual annotations of Leiden clusters computed separately within each of four lineages (B cells, CD4 T cells, CD8 T and NK cells, mononuclear phagocytes). For each lineage, PCA scores were aligned across batches with Harmony, each cell was connected to its 50 nearest neighbors, and the Leiden algorithm was run on that graph. Clusters were annotated by hand from marker genes (one-vs-rest AUC of 0.7 or more and pseudobulk FDR below 0.05), cross-referenced with published immune cell signatures and with CITE-seq surface protein data. Each label combines the lineage with the marker genes chosen when the labels were made; some subsets were renamed later in the paper, so the synonyms field lists the paper's subset ID (e.g., MP-12) and later name for each label. Cell Ontology terms were assigned in October 2026 from the marker statistics and the paper's interpretation of each subset.

Annotation method

manual

Cell Relationships