PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
Emma S Hoffmann1, Lara Hombrecher1, Ian F Diks1
1Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
Nucleic Acids Research
|November 24, 2025
Summary
PBMCpedia harmonizes single-cell data from over 4.3 million peripheral blood mononuclear cells (PBMCs) across 24 studies. This standardized resource enables cross-disease immune profiling and discovery.
Area of Science:
- Immunology
- Bioinformatics
- Genomics
Background:
- Single-cell transcriptomics of PBMCs provides insights into immune states.
- Integrating data from diverse studies is challenging due to preprocessing and annotation variations.
Purpose of the Study:
- To create a harmonized, publicly accessible resource for cross-study analysis of PBMC data.
- To facilitate immune profiling across various disease contexts and demographic groups.
Main Methods:
- Uniformly reprocessed 519 PBMC samples from 24 studies using a standardized pipeline.
- Applied consistent quality control and hierarchical cell type annotation.
- Integrated transcriptomic, T-cell receptor/B-cell receptor repertoire, and surface protein data.
Main Results:
- PBMCpedia includes over 4.3 million cells across 14 disease contexts and healthy controls.
- Supports metadata-aware comparisons across diseases, cell types, sexes, and age groups.
- Provides an interactive web interface for data exploration and querying.
Conclusions:
- PBMCpedia offers a transparent, harmonized, and disease-diverse PBMC resource.
- Enables integrative immune profiling at transcriptomic and proteogenomic levels.
- Facilitates cross-study immune discovery and understanding of immune states.
