TL;DR
This chapter presents a step-by-step guide to ChAseR, an R package to analyze chromatin architecture using network-based approaches, and illustrates the workflow on a promoter-centered chromatin network derived from human monocytes.
This chapter describes an optimized in situ Hi-C protocol tailored for cancer cell lines using MboI digestion and biotin-mediated pull-down to generate high-complexity libraries and outlines a computational workflow that extends beyond standard topological mapping of compartments and topologically associating domains t...
A detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling is provided.
This chapter examines how 3C technologies have refined the understanding of genome organization and gene regulation and supports a model in which genome folding is governed by the biophysical properties of chromatin.
Abstract Motivation Despite the growing use of HiChIP to investigate protein-directed chromatin architecture, a comprehensive and reproducible pipeline for analysing these datasets-from raw reads to multiscale 3D genome features-remains lacking. Existing tools often focus on isolated components, such as loop calling or...
The protocols for ChIP-seq are outlined, including immunoprecipitation, library preparation for high-throughput sequencing, and bioinformatics analysis of sequencing data that the authors routinely perform in their lab groups, and include troubleshooting tips for each step.
HisTrader is presented, a computational approach that identifies nucleosome-free regions (NFRs) within ChIP-based profiling of histone modification peaks, which reduces the target sequence length for motif discovery and genetic variant prioritization.
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