Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis)
Abstract Background Commercially available Illumina DNA methylation arrays (HumanMethylation 27K, HumanMethylation450, and MethylationEPIC BeadChip) can be used for comprehensive DNA methylation analyses of not only the human genome but also other mammalian genomes, ranging from those of nonhuman pr...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2020-12-01
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| Series: | Neuropsychopharmacology Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/npr2.12145 |
| _version_ | 1811177975672995840 |
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| author | Yutaka Nakachi Kazuhiro Ishii Miki Bundo Tomoyuki Masuda Kazuya Iwamoto |
| author_facet | Yutaka Nakachi Kazuhiro Ishii Miki Bundo Tomoyuki Masuda Kazuya Iwamoto |
| author_sort | Yutaka Nakachi |
| collection | DOAJ |
| description | Abstract Background Commercially available Illumina DNA methylation arrays (HumanMethylation 27K, HumanMethylation450, and MethylationEPIC BeadChip) can be used for comprehensive DNA methylation analyses of not only the human genome but also other mammalian genomes, ranging from those of nonhuman primates to those of rodents. However, practical application of the EPIC array to the crab‐eating macaque has not been reported. Methods Through bioinformatic analyses involving cross‐species comparison and consideration of probe performance, we selected array probes that can be reliably used for the crab‐eating macaque genome. A DNA methylation assay using an EPIC array was performed on genomic DNA extracted from the brains of five crab‐eating macaques. The obtained DNA methylation data were compared with a publicly available dataset. Results Among the 865 918 probes in the EPIC array, a total of 183 509 probes (21.2%) were selected as high‐confidence array probes in the crab‐eating macaque. Subsequent comparisons revealed that the data from these probes showed good concordance with other DNA methylation datasets of the crab‐eating macaque. Conclusion The selected high‐confidence array probes would be useful for high‐throughput DNA methylation assays of the crab‐eating macaque. |
| first_indexed | 2024-04-11T06:10:25Z |
| format | Article |
| id | doaj.art-0934bac1661749859d6b1c19a8202e55 |
| institution | Directory Open Access Journal |
| issn | 2574-173X |
| language | English |
| last_indexed | 2024-04-11T06:10:25Z |
| publishDate | 2020-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | Neuropsychopharmacology Reports |
| spelling | doaj.art-0934bac1661749859d6b1c19a8202e552022-12-22T04:41:16ZengWileyNeuropsychopharmacology Reports2574-173X2020-12-0140442342610.1002/npr2.12145Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis)Yutaka Nakachi0Kazuhiro Ishii1Miki Bundo2Tomoyuki Masuda3Kazuya Iwamoto4Department of Molecular Brain Science Graduate School of Medical Sciences Kumamoto University Kumamoto JapanDepartment of Neurology Faculty of Medicine University of Tsukuba Ibaraki JapanDepartment of Molecular Brain Science Graduate School of Medical Sciences Kumamoto University Kumamoto JapanDepartment of Neurology Faculty of Medicine University of Tsukuba Ibaraki JapanDepartment of Molecular Brain Science Graduate School of Medical Sciences Kumamoto University Kumamoto JapanAbstract Background Commercially available Illumina DNA methylation arrays (HumanMethylation 27K, HumanMethylation450, and MethylationEPIC BeadChip) can be used for comprehensive DNA methylation analyses of not only the human genome but also other mammalian genomes, ranging from those of nonhuman primates to those of rodents. However, practical application of the EPIC array to the crab‐eating macaque has not been reported. Methods Through bioinformatic analyses involving cross‐species comparison and consideration of probe performance, we selected array probes that can be reliably used for the crab‐eating macaque genome. A DNA methylation assay using an EPIC array was performed on genomic DNA extracted from the brains of five crab‐eating macaques. The obtained DNA methylation data were compared with a publicly available dataset. Results Among the 865 918 probes in the EPIC array, a total of 183 509 probes (21.2%) were selected as high‐confidence array probes in the crab‐eating macaque. Subsequent comparisons revealed that the data from these probes showed good concordance with other DNA methylation datasets of the crab‐eating macaque. Conclusion The selected high‐confidence array probes would be useful for high‐throughput DNA methylation assays of the crab‐eating macaque.https://doi.org/10.1002/npr2.12145bisulfite modificationcynomolgus monkeycytosineDNA methylationnonhuman primate |
| spellingShingle | Yutaka Nakachi Kazuhiro Ishii Miki Bundo Tomoyuki Masuda Kazuya Iwamoto Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) Neuropsychopharmacology Reports bisulfite modification cynomolgus monkey cytosine DNA methylation nonhuman primate |
| title | Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) |
| title_full | Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) |
| title_fullStr | Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) |
| title_full_unstemmed | Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) |
| title_short | Use of the Illumina EPIC methylation array for epigenomic research in the crab‐eating macaque (Macaca fascicularis) |
| title_sort | use of the illumina epic methylation array for epigenomic research in the crab eating macaque macaca fascicularis |
| topic | bisulfite modification cynomolgus monkey cytosine DNA methylation nonhuman primate |
| url | https://doi.org/10.1002/npr2.12145 |
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