scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species

Author:

Qian Feng-Cui123,Zhou Li-Wei4,Zhu Yan-Bing5,Li Yan-Yu6,Yu Zheng-Min7,Feng Chen-Chen6,Fang Qiao-Li7,Zhao Yu7,Cai Fu-Hong7,Wang Qiu-Yu3,Tang Hui-Fang18910,Li Chun-Quan111273ORCID

Affiliation:

1. The 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

2. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

3. The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

4. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing, China

5. Beijing Clinical Research Institute, Beijing Friendship Hospital, Capital Medical University , Beijing, China

6. School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China

7. School of Computer, University of South China , Hengyang, Hunan, 421001, China

8. The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

9. The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School , Hengyang, China

10. , University of South China , Hengyang, China

11. Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China

Abstract

Abstract Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

Funder

National Natural Science Foundation of China

Natural Science Foundation of Hunan Province

Natural Science Foundation of Heilongjiang Province

Research Foundation of the First Affiliated Hospital of University of South China

University of South China

Scientific Research Fund Project of Hunan Provincial Health Commission

Hunan Provincial Science and Technology Innovation

Special Funds for the Construction of Innovative Provinces in Hunan

Research Foundation of Education Bureau of Hunan Province

Publisher

Oxford University Press (OUP)

Subject

Genetics

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