Chromatin Accessibility, 1st ed. 2023 Methods and Protocols Methods in Molecular Biology Series, Vol. 2611

Part I: Bulk Cleavage-Based Methods

1. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-Seq

            Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, and William J. Greenleaf

2. Mapping Nucleosome Location Using FS-Seq

3. NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells

            Hang Gyeong Chin, Udayakumar S. Vishnu, Zhiyi Sun, V.K. Chaithanya Ponnaluri, Guoqiang Zhang, Shuang-yong Xu, Touati Benoukraf, Paloma Cejas, George Spracklin, Pierre-Olivier Estève, Henry W. Long, and Sriharsa Pradhan

4. Measuring Inaccessible Chromatin Genome-Wide Using Protect-Seq

            George Spracklin, Liyan Yang, Sriharsa Pradhan, and Job Dekker

5. Determination of the Chromatin Openness in Bacterial Genomes

            Mahmoud M. Al-Bassam and Karsten Zengler

6. Profiling Chromatin Accessibility on Replicated DNA with Repli-ATAC-Seq

            Kathleen R. Stewart-Morgan and Anja Groth

7. Analysis of Chromatin Interaction and Accessibility by Trac-Looping

            Shuai Liu, Qingsong Tang, and Keji Zhao

Part II: Methods for Measuring the Absolute Levels of Occupancy/Accessibility

8. Single-Molecule Mapping of Chromatin Accessiility Using NOMe-Seq/dSMF

            Michaela Hinks, Georgi K. Marinov, Anshul Kundaje, Lacramioara Bintu, and William J. Greenleaf

9. ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities

            Elisa Oberbeckmann, Michael Roland Wolff, Nils Krietenstein, Mark Heron, Andrea Schmid, Tobias Straub, Ulrich Gerland, and Philipp Korber

Part III: Methods for Profiling Chromatin Accessibility at the Single-Cell Level

10. Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq

            Chenxu Zhu, Zhaoning Wang, and Bing Ren

11. Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-Seq

            Samuel H. Kim, Georgi K. Marinov, S. Tansu Bagdatli, Soon Il Higashino, Zohar Shipony, Anshul Kundaje, and William J. Greenleaf

12. Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq

            Michael Wasney and Sebastian Pott

13. Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq

            Eleni Mimitou, Peter Smibert, and Caleb A. Lareau

14. Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq

            Leif S. Ludwig and Caleb A. Lareau

Part IV: Imaging Methods for Visualization of Accessible DNA

15. ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with Imaging

            Yonglong Dang, Ram Prakash Yadav, and Xingqi Chen

16. NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells

            Pierre-Olivier Estève, Udayakumar S. Vishnu, Hang Gyeong Chin, and Sriharsa Pradhan

Part V: Computational Analysis of Chromatin Accessibility Datasets

17. ATAC-Seq Data Processing

            Daniel Kim

18. Deep Learning on Chromatin Accessibility

            Daniel Kim

Includes cutting-edge techniques

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts