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 b y unif ormly reprocessing 519 samples (o v er 4.3 million cells) from 24 publicly a v ailable 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 neurodegenerativ e disorders, as w ell as health y controls, PBMCpedia supports met adat a-a w are comparisons across diseases, cell types, se x es, 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 le v els. To support exploration and accessibility, we provide an interactiv e w eb interf ace ( https://w eb.ccb.uni-saarland.de/pbmcpedia/) f or querying gene e xpression, mark er genes, and pathw a y enrichment across cell types, conditions, se x es, 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.