Chromatin Accessibility : Methods and Protocols / edited by Georgi K. Marinov, William J. Greenleaf.

Format:

Book

Contributor:

Marinov, Georgi K., Editor.

Greenleaf, William J., Editor.

Series:

Methods in Molecular Biology, 1940-6029 ; 2611

Language:

English

Subjects (All):

Chromosomes.

Biology--Technique.

Biology.

Genetics.

Genetic Techniques.

Genetics and Genomics.

Local Subjects:

Chromosomes.

Genetic Techniques.

Genetics and Genomics.

Physical Description:

1 online resource (XI, 341 p. 57 illus., 50 illus. in color.)

Edition:

1st ed. 2023.

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2023.

Summary:

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.

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.

ISBN:

9781071628997

1071628992