DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos
Summary: Cell-free DNA (cfDNA) in spent embryo culture media (SECM) provides prospects for noninvasive preimplantation genetic testing. Here, we present a post-bisulfite-adapter-tagging (PBAT)-based whole-genome DNA methylation sequencing protocol (SECM-PBAT) for human SECM cfDNA analysis. We descri...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723002058 |
| _version_ | 1797842238603001856 |
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| author | Yuan Gao Yidong Chen Jie Qiao Jin Huang Lu Wen |
| author_facet | Yuan Gao Yidong Chen Jie Qiao Jin Huang Lu Wen |
| author_sort | Yuan Gao |
| collection | DOAJ |
| description | Summary: Cell-free DNA (cfDNA) in spent embryo culture media (SECM) provides prospects for noninvasive preimplantation genetic testing. Here, we present a post-bisulfite-adapter-tagging (PBAT)-based whole-genome DNA methylation sequencing protocol (SECM-PBAT) for human SECM cfDNA analysis. We describe steps for SECM lysis, bisulfite conversion and purification, preamplification by random priming, tagging adapter II, and library establishment. We then detail library quality control, sequencing, and bioinformatics analysis. This approach simultaneously detects chromosome aneuploidy and deduces the proportional contributions of cellular components.For complete details on the use and execution of this protocol, please refer to Chen et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-09T16:44:42Z |
| format | Article |
| id | doaj.art-64e99efa11e24ec6b3b4e9f79a948fd0 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-09T16:44:42Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-64e99efa11e24ec6b3b4e9f79a948fd02023-04-23T06:07:50ZengElsevierSTAR Protocols2666-16672023-06-0142102247DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryosYuan Gao0Yidong Chen1Jie Qiao2Jin Huang3Lu Wen4Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Corresponding authorBiomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, China; Corresponding authorBiomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, ChinaBiomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100871, China; Corresponding authorBiomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing 100871, China; Corresponding authorSummary: Cell-free DNA (cfDNA) in spent embryo culture media (SECM) provides prospects for noninvasive preimplantation genetic testing. Here, we present a post-bisulfite-adapter-tagging (PBAT)-based whole-genome DNA methylation sequencing protocol (SECM-PBAT) for human SECM cfDNA analysis. We describe steps for SECM lysis, bisulfite conversion and purification, preamplification by random priming, tagging adapter II, and library establishment. We then detail library quality control, sequencing, and bioinformatics analysis. This approach simultaneously detects chromosome aneuploidy and deduces the proportional contributions of cellular components.For complete details on the use and execution of this protocol, please refer to Chen et al. (2021).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/S2666166723002058BioinformaticsSequence AnalysisCell BiologySequencing |
| spellingShingle | Yuan Gao Yidong Chen Jie Qiao Jin Huang Lu Wen DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos STAR Protocols Bioinformatics Sequence Analysis Cell Biology Sequencing |
| title | DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos |
| title_full | DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos |
| title_fullStr | DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos |
| title_full_unstemmed | DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos |
| title_short | DNA methylation protocol for analyzing cell-free DNA in the spent culture medium of human preimplantation embryos |
| title_sort | dna methylation protocol for analyzing cell free dna in the spent culture medium of human preimplantation embryos |
| topic | Bioinformatics Sequence Analysis Cell Biology Sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723002058 |
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