Titlebook: Computational Methods for 3D Genome Analysis; Ryuichiro Nakato Book 2025 The Editor(s) (if applicable) and The Author(s), under exclusive

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Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPyentire workflow from FASTQ mapping to visualization. In this chapter, we demonstrate how to analyze and visualize Hi-C data using CustardPy and introduce several 3D genome features observed in Hi-C data.

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Single-Cell Hi-C Analysis Workflow with PairtoolsThis educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.

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Prophylaxis

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Radiologische Notfalldiagnostik des Abdomensave been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolution. In this chapter, I provide a basic method for Micro-C analysis. I present and discuss a series of data analyses ranging from mapping to basic downstream analyses, including loop detection.

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https://doi.org/10.1007/978-3-662-61508-9t and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.

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Gespr?ch mit Angelika Freifrau von Fritschd comparing structures effectively depending on the characteristics of the genome or cell type. Here, we describe a method for acquiring Hi-C data from medaka early embryos and quantifying the structural changes during the developmental process.

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Meditate

Erstversorgung durch den Krankenhausarztnd prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop?extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.

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