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Related Experiment Video

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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
PubMed
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.

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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.