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 Barry Milavetz, Brenna Hanson, Kincaid Rowbotham, and Jacob Haugen 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.