Titlebook: Chromatin Accessibility; Methods and Protocol Georgi K. Marinov,William J. Greenleaf Book 2023 The Editor(s) (if applicable) and The Author

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ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with ImagingAssay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that enables direct imaging of the accessible genome in situ and deep sequencing to reveal the identity of the imaged elements. Here we image spatial organization of the accessible genome in HT1080 cells with this method.

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Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seqturned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (.ssay for .ransposase-.ccessible .hromati

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Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cellsssible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-c

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Determination of the Chromatin Openness in Bacterial Genomesgulation in the chromatins of eukaryotic cells. Here, we describe POP-seq (.rokaryotic chromatin .penness .rofiling .uencing), an adaptation of the ATAC-seq method, to interrogate changes in the openness of prokaryotic nucleoids.

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Analysis of Chromatin Interaction and Accessibility by Trac-Loopingcture and its role in regulating cell activities. To examine the genome-wide chromatin interactions at accessible chromatin regions, we developed a DNA transposase-mediated analysis of chromatin looping (Trac-looping) method for simultaneously detecting chromatin interactions and chromatin accessibi