| Summary: | 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.
|
|---|