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

SUBMITTER: Hoffmann ES 

PROVIDER: S-EPMC12807695 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature