PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation

Abstract Single-cell transcriptomic studies of peripheral blood mononuclear cells (PBMCs) offer valuable insights into immune states across diverse biological conditions, yet cross-study integration remains difficult due to divergent preprocessing and annotations. PBMCpedia addresses this by uniformly reprocessing 519 samples (over 4.3 million cells) from 24 publicly available single-cell RNA sequencing studies using a standardized pipeline with consistent quality control and hierarchical cell type annotation. Spanning 14 disease contexts, including autoimmune, infectious, and neurodegenerative disorders, as well as healthy controls, PBMCpedia supports metadata-aware comparisons across diseases, cell types, sexes, and age groups. It also includes T-cell receptor/B-cell receptor repertoire data for 75 samples and surface protein measurements for 56 samples, enabling integrative immune profiling at both the transcriptomic and proteogenomic levels. To support exploration and accessibility, we provide an interactive web interface (https://web.ccb.uni-saarland.de/pbmcpedia/) for querying gene expression, marker genes, and pathway enrichment across cell types, conditions, sexes, and age groups. PBMCpedia fills a critical gap by offering a transparent, harmonized, and disease-diverse PBMC resource designed for cross-study immune profiling and discovery.