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

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

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...

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Bibliographic Details
Main Authors: Haiyan Gong, Minghong Li, Mengdie Ji, Xiaotong Zhang, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, Yang Chen
Format: Article
Language:English
Published: Elsevier 2023-06-01
Series:STAR Protocols
Subjects:
Bioinformatics
Sequence Analysis
Sequencing
ChIPseq
Gene Expression
Biotechnology and Bioengineering
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166723001466

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