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scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species
Feng-Cui Qian1,2,3, Li-Wei Zhou4, Yan-Bing Zhu5
1The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
Nucleic Acids Research
|October 28, 2023
Summary
scATAC-Ref is a new database of single-cell chromatin accessibility profiles with cell labels. This resource aids in accurately assigning cell types for biological and pathological insights.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Single-cell chromatin accessibility (scATAC-seq) reveals cell-specific regulatory programs.
- Accurate cell type assignment is crucial but challenging in scATAC-seq data.
- Understanding cell identity is key for biological and pathological insights.
Purpose of the Study:
- To create a comprehensive, manually curated database of scATAC-seq profiles with known cell labels.
- To facilitate accurate cell type assignment and exploration of epigenetic regulation.
- To provide a high-quality resource for the scientific community.
Main Methods:
- Extensive literature review to curate scATAC-seq data.
- Development of the scATAC-Ref database with over 1.6 million cells.
- Standardized downstream analysis including gene activity, TF enrichment, and co-accessibility.
Main Results:
- scATAC-Ref contains 1,694,372 cells with known labels across >400 cell/tissue types and five species.
- Comprehensive analyses reveal gene activity, TF enrichment, differential regions, and pathway information.
- A user-friendly interface allows querying, browsing, and visualization of cell types.
Conclusions:
- scATAC-Ref is a valuable resource for exploring epigenetic regulation across diverse cell types.
- The database supports accurate cell type identification and functional dissection.
- Facilitates research in cell origin, evolution, and disease.
