scBlood: A comprehensive single-cell accessible chromatin database of blood cells

Yu Zhao; Zheng-Min Yu; Ting Cui; Li-Dong Li; Yan-Yu Li; Feng-Cui Qian; Li-Wei Zhou; Ye Li; Qiao-Li Fang; Xue-Mei Huang; Qin-Yi Zhang; Fu-Hong Cai; Fu-Juan Dong; De-Si Shang; Chun-Quan Li; Qiu-Yu Wang

Computational and Structural Biotechnology Journal (Dec 2024)

scBlood: A comprehensive single-cell accessible chromatin database of blood cells

Yu Zhao,
Zheng-Min Yu,
Ting Cui,
Li-Dong Li,
Yan-Yu Li,
Feng-Cui Qian,
Li-Wei Zhou,
Ye Li,
Qiao-Li Fang,
Xue-Mei Huang,
Qin-Yi Zhang,
Fu-Hong Cai,
Fu-Juan Dong,
De-Si Shang,
Chun-Quan Li,
Qiu-Yu Wang

Affiliations

Yu Zhao: The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; School of Computer, University of South China, Hengyang, Hunan 421001, China
Zheng-Min Yu: School of Computer, University of South China, Hengyang, Hunan 421001, China
Ting Cui: The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
Li-Dong Li: School of Computer, University of South China, Hengyang, Hunan 421001, China
Yan-Yu Li: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
Feng-Cui Qian: The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
Li-Wei Zhou: State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
Ye Li: Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
Qiao-Li Fang: School of Computer, University of South China, Hengyang, Hunan 421001, China
Xue-Mei Huang: School of Computer, University of South China, Hengyang, Hunan 421001, China
Qin-Yi Zhang: Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
Fu-Hong Cai: School of Computer, University of South China, Hengyang, Hunan 421001, China
Fu-Juan Dong: School of Computer, University of South China, Hengyang, Hunan 421001, China
De-Si Shang: The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Corresponding author.
Chun-Quan Li: The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; School of Computer, University of South China, Hengyang, Hunan 421001, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; 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; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Corresponding author at: The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Qiu-Yu Wang: School of Computer, University of South China, Hengyang, Hunan 421001, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; 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; Corresponding author at: School of Computer, University of South China, Hengyang, Hunan 421001, China.

Journal volume & issue: Vol. 23
pp. 2746 – 2753

Abstract

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The advent of single cell transposase-accessible chromatin sequencing (scATAC-seq) technology enables us to explore the genomic characteristics and chromatin accessibility of blood cells at the single-cell level. To fully make sense of the roles and regulatory complexities of blood cells, it is critical to collect and analyze these rapidly accumulating scATAC-seq datasets at a system level. Here, we present scBlood (https://bio.liclab.net/scBlood/), a comprehensive single-cell accessible chromatin database of blood cells. The current version of scBlood catalogs 770,907 blood cells and 452,247 non-blood cells from ∼400 high-quality scATAC-seq samples covering 30 tissues and 21 disease types. All data hosted on scBlood have undergone preprocessing from raw fastq files and multiple standards of quality control. Furthermore, we conducted comprehensive downstream analyses, including multi-sample integration analysis, cell clustering and annotation, differential chromatin accessibility analysis, functional enrichment analysis, co-accessibility analysis, gene activity score calculation, and transcription factor (TF) enrichment analysis. In summary, scBlood provides a user-friendly interface for searching, browsing, analyzing, visualizing, and downloading scATAC-seq data of interest. This platform facilitates insights into the functions and regulatory mechanisms of blood cells, as well as their involvement in blood-related diseases.

Published in Computational and Structural Biotechnology Journal

ISSN: 2001-0370 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Technology: Chemical technology: Biotechnology
Website: https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal

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