Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell line

Haiyan Gong; Minghong Li; Mengdie Ji; Xiaotong Zhang; Zan Yuan; Sichen Zhang; Yi Yang; Chun Li; Yang Chen

STAR Protocols (Jun 2023)

Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell line

Haiyan Gong,
Minghong Li,
Mengdie Ji,
Xiaotong Zhang,
Zan Yuan,
Sichen Zhang,
Yi Yang,
Chun Li,
Yang Chen

Affiliations

Haiyan Gong: Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
Minghong Li: Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
Mengdie Ji: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
Xiaotong Zhang: Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China; Shunde Innovation School, University of Science and Technology Beijing, Foshan 528399, China; Corresponding author
Zan Yuan: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
Sichen Zhang: Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
Yi Yang: Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
Chun Li: School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
Yang Chen: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China; Corresponding author

Journal volume & issue: Vol. 4, no. 2
p. 102188

Abstract

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Summary: Here, we present a protocol for calculating the spatial density of regulatory chromatin interactions (SD-RCI) using Hi-C, ATAC-seq, and ChIP-seq datasets from the same cell line. We describe steps for selecting and preprocessing datasets, training and predicting a model to obtain regulatory chromatin interactions, and evaluating model performance. We then detail calculation of SD-RCI and visualization of the correlation between SD-RCI and gene expression. This protocol is applicable to Hi-C, ATAC-seq, and ChIP-seq data from the human cell line.For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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