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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.
List of contents
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.
