An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons
Summary: ATAC-seq is a versatile, adaptable, and widely adopted technique for mapping open chromatin regions. However, some biological systems, such as primary neurons, present unique challenges to its application. Conventional ATAC-seq would require the dissociation of the primary neurons after pla...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166721005608 |
| _version_ | 1819174329210896384 |
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| author | Maya Maor-Nof Zohar Shipony Georgi K. Marinov William J. Greenleaf Aaron D. Gitler |
| author_facet | Maya Maor-Nof Zohar Shipony Georgi K. Marinov William J. Greenleaf Aaron D. Gitler |
| author_sort | Maya Maor-Nof |
| collection | DOAJ |
| description | Summary: ATAC-seq is a versatile, adaptable, and widely adopted technique for mapping open chromatin regions. However, some biological systems, such as primary neurons, present unique challenges to its application. Conventional ATAC-seq would require the dissociation of the primary neurons after plating but dissociating them leads to rapid cell death and major changes in cell state, affecting ATAC-seq results. We have developed this modified ATAC-seq protocol to address this challenge for primary neurons, providing a high-quality and high-resolution accessible chromatin profile.For complete details on the use and execution of this protocol, please refer to Maor-Nof et al. (2021). |
| first_indexed | 2024-12-22T20:37:14Z |
| format | Article |
| id | doaj.art-6a71d137cfde4b6c812c6b4c470a196a |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-22T20:37:14Z |
| publishDate | 2021-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-6a71d137cfde4b6c812c6b4c470a196a2022-12-21T18:13:26ZengElsevierSTAR Protocols2666-16672021-12-0124100854An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neuronsMaya Maor-Nof0Zohar Shipony1Georgi K. Marinov2William J. Greenleaf3Aaron D. Gitler4Department of Genetics, Stanford University, Stanford, CA 94305, USA; Corresponding authorDepartment of Genetics, Stanford University, Stanford, CA 94305, USADepartment of Genetics, Stanford University, Stanford, CA 94305, USADepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USADepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Corresponding authorSummary: ATAC-seq is a versatile, adaptable, and widely adopted technique for mapping open chromatin regions. However, some biological systems, such as primary neurons, present unique challenges to its application. Conventional ATAC-seq would require the dissociation of the primary neurons after plating but dissociating them leads to rapid cell death and major changes in cell state, affecting ATAC-seq results. We have developed this modified ATAC-seq protocol to address this challenge for primary neurons, providing a high-quality and high-resolution accessible chromatin profile.For complete details on the use and execution of this protocol, please refer to Maor-Nof et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166721005608GeneticsGenomicsSequencingMolecular BiologyNeuroscience |
| spellingShingle | Maya Maor-Nof Zohar Shipony Georgi K. Marinov William J. Greenleaf Aaron D. Gitler An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons STAR Protocols Genetics Genomics Sequencing Molecular Biology Neuroscience |
| title | An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons |
| title_full | An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons |
| title_fullStr | An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons |
| title_full_unstemmed | An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons |
| title_short | An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons |
| title_sort | optimized atac seq protocol for genome wide mapping of active regulatory elements in primary mouse cortical neurons |
| topic | Genetics Genomics Sequencing Molecular Biology Neuroscience |
| url | http://www.sciencedirect.com/science/article/pii/S2666166721005608 |
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