Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alte...
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2017
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| Online Access: | http://hdl.handle.net/1721.1/109400 https://orcid.org/0000-0003-0250-0474 https://orcid.org/0000-0001-6913-4910 https://orcid.org/0000-0001-5230-3626 https://orcid.org/0000-0002-6804-251X https://orcid.org/0000-0001-9249-8181 |
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| author | Shelley, Brandon C. Mandefro, Berhan Sareen, Dhruv Svendsen, Clive N. Milani, Pamela Escalante, Renan A. Patel-Murray, Natasha Leanna Xin, Xiaofeng Adam, Miriam Fraenkel, Ernest |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Shelley, Brandon C. Mandefro, Berhan Sareen, Dhruv Svendsen, Clive N. Milani, Pamela Escalante, Renan A. Patel-Murray, Natasha Leanna Xin, Xiaofeng Adam, Miriam Fraenkel, Ernest |
| author_sort | Shelley, Brandon C. |
| collection | MIT |
| description | In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alter chromatin structure, especially in fragile cells such as neurons. Our aim was to develop a protocol for freezing neuronal cells that is compatible with ATAC-Seq; we focused on a disease-relevant cell type, namely motor neurons differentiated from induced pluripotent stem cells (iMNs) from a patient affected by spinal muscular atrophy. We found that while flash-frozen iMNs are not suitable for ATAC-Seq, the assay is successful with slow-cooled cryopreserved cells. Using this method, we were able to isolate high quality, intact nuclei, and we verified that epigenetic results from fresh and cryopreserved iMNs quantitatively agree. |
| first_indexed | 2024-09-23T15:16:11Z |
| format | Article |
| id | mit-1721.1/109400 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:16:11Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1094002022-09-29T13:49:21Z Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells Shelley, Brandon C. Mandefro, Berhan Sareen, Dhruv Svendsen, Clive N. Milani, Pamela Escalante, Renan A. Patel-Murray, Natasha Leanna Xin, Xiaofeng Adam, Miriam Fraenkel, Ernest Massachusetts Institute of Technology. Computational and Systems Biology Program Massachusetts Institute of Technology. Department of Biological Engineering Milani, Pamela Escalante, Renan A. Patel-Murray, Natasha Leanna Xin, Xiaofeng Adam, Miriam Fraenkel, Ernest In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alter chromatin structure, especially in fragile cells such as neurons. Our aim was to develop a protocol for freezing neuronal cells that is compatible with ATAC-Seq; we focused on a disease-relevant cell type, namely motor neurons differentiated from induced pluripotent stem cells (iMNs) from a patient affected by spinal muscular atrophy. We found that while flash-frozen iMNs are not suitable for ATAC-Seq, the assay is successful with slow-cooled cryopreserved cells. Using this method, we were able to isolate high quality, intact nuclei, and we verified that epigenetic results from fresh and cryopreserved iMNs quantitatively agree. National Institutes of Health (U.S.) (U54-NS-091046) National Institutes of Health (U.S.) (U01-CA-184898) 2017-05-26T23:40:28Z 2017-05-26T23:40:28Z 2016-05 2016-02 Article http://purl.org/eprint/type/JournalArticle 2045-2322 http://hdl.handle.net/1721.1/109400 Milani, Pamela et al. “Cell Freezing Protocol Suitable for ATAC-Seq on Motor Neurons Derived from Human Induced Pluripotent Stem Cells.” Scientific Reports 6.1 (2016): n. pag. https://orcid.org/0000-0003-0250-0474 https://orcid.org/0000-0001-6913-4910 https://orcid.org/0000-0001-5230-3626 https://orcid.org/0000-0002-6804-251X https://orcid.org/0000-0001-9249-8181 en_US http://dx.doi.org/10.1038/srep25474 Scientific Reports Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Scientific Reports |
| spellingShingle | Shelley, Brandon C. Mandefro, Berhan Sareen, Dhruv Svendsen, Clive N. Milani, Pamela Escalante, Renan A. Patel-Murray, Natasha Leanna Xin, Xiaofeng Adam, Miriam Fraenkel, Ernest Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title | Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title_full | Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title_fullStr | Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title_full_unstemmed | Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title_short | Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells |
| title_sort | cell freezing protocol suitable for atac seq on motor neurons derived from human induced pluripotent stem cells |
| url | http://hdl.handle.net/1721.1/109400 https://orcid.org/0000-0003-0250-0474 https://orcid.org/0000-0001-6913-4910 https://orcid.org/0000-0001-5230-3626 https://orcid.org/0000-0002-6804-251X https://orcid.org/0000-0001-9249-8181 |
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