Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens
Summary: Aberrant DNA methylation is a universal feature of cancer. Here, we present a protocol for generating high-quality genome-scale DNA methylation sequencing data from a variety of human cancer biospecimens including immortalized cell lines, fresh-frozen surgical resections, and formalin-fixed...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723006810 |
| _version_ | 1827764850926813184 |
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| author | Euan J. Rodger Peter A. Stockwell Suzan Almomani Michael R. Eccles Aniruddha Chatterjee |
| author_facet | Euan J. Rodger Peter A. Stockwell Suzan Almomani Michael R. Eccles Aniruddha Chatterjee |
| author_sort | Euan J. Rodger |
| collection | DOAJ |
| description | Summary: Aberrant DNA methylation is a universal feature of cancer. Here, we present a protocol for generating high-quality genome-scale DNA methylation sequencing data from a variety of human cancer biospecimens including immortalized cell lines, fresh-frozen surgical resections, and formalin-fixed paraffin-embedded tissues. We describe steps for DNA extraction considerations, reduced representation bisulfite sequencing, data processing and quality control, and downstream data analysis and integration. This protocol is also applicable for other human diseases and methylome profiling in other organisms.For complete details on the use and execution of this protocol, please refer to Rodger et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-11T11:10:43Z |
| format | Article |
| id | doaj.art-9183b74f093446f493bf266bd8422511 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-11T11:10:43Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-9183b74f093446f493bf266bd84225112023-11-12T04:41:01ZengElsevierSTAR Protocols2666-16672023-12-0144102714Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimensEuan J. Rodger0Peter A. Stockwell1Suzan Almomani2Michael R. Eccles3Aniruddha Chatterjee4Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Corresponding authorDepartment of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New ZealandDepartment of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New ZealandDepartment of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New ZealandDepartment of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Honorary Professor, UPES University, Dehradun, India; Corresponding authorSummary: Aberrant DNA methylation is a universal feature of cancer. Here, we present a protocol for generating high-quality genome-scale DNA methylation sequencing data from a variety of human cancer biospecimens including immortalized cell lines, fresh-frozen surgical resections, and formalin-fixed paraffin-embedded tissues. We describe steps for DNA extraction considerations, reduced representation bisulfite sequencing, data processing and quality control, and downstream data analysis and integration. This protocol is also applicable for other human diseases and methylome profiling in other organisms.For complete details on the use and execution of this protocol, please refer to Rodger et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723006810BioinformaticsSequence analysisCancerGenomicsSequencingMolecular Biology |
| spellingShingle | Euan J. Rodger Peter A. Stockwell Suzan Almomani Michael R. Eccles Aniruddha Chatterjee Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens STAR Protocols Bioinformatics Sequence analysis Cancer Genomics Sequencing Molecular Biology |
| title | Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens |
| title_full | Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens |
| title_fullStr | Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens |
| title_full_unstemmed | Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens |
| title_short | Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens |
| title_sort | protocol for generating high quality genome scale dna methylation sequencing data from human cancer biospecimens |
| topic | Bioinformatics Sequence analysis Cancer Genomics Sequencing Molecular Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723006810 |
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