Human PBMC atlas - T CD8 effector and nonnaive cells and innate lymphoid cells including NK cells

Cell annotations were generated through iterative hierarchical clustering. Broad lineages were first identified and then recursively subdivided into finer sublineages and sub-sublineages (e.g., T → CD4 T → Effector CD4 T). Clusters were iteratively re-clustered at multiple resolutions, split or merged based on biological evidence, and refined through repeated quality-control steps. Final annotations were determined by consensus of an international group using canonical marker genes, one-vs-all and all-vs-all differential expression analyses, and cluster relationships within the hierarchical framework. Low-quality cells, doublets, and contaminating populations were identified and removed throughout the annotation process; following each round of removal, datasets were reprocessed and re-clustered to improve cluster resolution and biological consistency before subsequent annotation refinement.