Chromatin Accessibility

Methods and Protocols

Georgi K. Marinov, William J. Greenleaf (Herausgeber)

Buch | Softcover

341 Seiten

2024 | 1st ed. 2023
Springer-Verlag New York Inc.
978-1-0716-2901-7 (ISBN)

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This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts.
Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Genome-Wide Mapping of Active Regulatory Elements Using ATAC-Seq.- Mapping Nucleosome Location Using FS-Seq.- NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.- Measuring Inaccessible Chromatin Genome-Wide Using Protect-Seq.- Determination of the Chromatin Openness in Bacterial Genomes.- Profiling Chromatin Accessibility on Replicated DNA with Repli-ATAC-Seq.- Analysis of Chromatin Interaction and Accessibility by Trac-Looping.- Single-Molecule Mapping of Chromatin Accessiility Using NOMe-Seq/dSMF.- ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities.- Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq.- Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-Seq.- Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq.- Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq.- Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq.- ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with Imaging.- NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.- ATAC-Seq Data Processing.- Deep Learning on Chromatin Accessibility.

Erscheinungsdatum	22.02.2024
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	50 Illustrations, color; 7 Illustrations, black and white; XI, 341 p. 57 illus., 50 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
	Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
	Naturwissenschaften ► Biologie ► Zellbiologie
Schlagworte	Accessible DNA • Chromatin biology • Enzymatic cleavage • gene expression • Nucleosome positioning • Single-cell genomics
ISBN-10	1-0716-2901-8 / 1071629018
ISBN-13	978-1-0716-2901-7 / 9781071629017
Zustand	Neuware