scImmOmics: a manually curated resource of single-cell multi-omics immune data

Area of Science:

• Immunology
• Bioinformatics
• Genomics

Background:

• Single-cell sequencing reveals diverse immune cell functions crucial for understanding health and disease.
• Existing single-cell RNA sequencing (scRNA-seq) data lacks a harmonized, immune-specific multi-omics atlas.

Purpose of the Study:

• To develop scImmOmics, a manually curated, single-cell multi-omics immune database.
• To provide a comprehensive resource for immune cell heterogeneity and regulatory mechanisms.

Main Methods:

• Collected and curated high-quality immune cells with known labels.
• Integrated data from seven single-cell sequencing technologies.
• Standardized immune cell nomenclature and created a hierarchical structure.

Main Results:

• scImmOmics contains over 2.9 million cell-type labeled immune cells across 131 types, 47 tissues, and 4 species.
• The database includes T-cell/B-cell receptor sequencing, cell-specific regulatory states, and cell-to-cell communication networks.
• Information on immune cell responses to cytokines is also provided.

Conclusions:

• scImmOmics serves as a valuable platform for exploring immune cell diversity and function.
• It facilitates the elucidation of specific regulatory mechanisms at the single-cell level.