ArticleBMC bioinformatics2017
Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 29 citations in OpenAlex.
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- Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer patient-derived xenografts.Nature communications · 2024Article
- DNA demethylation triggers cell free DNA release in colorectal cancer cells.Genome medicine · 2024Article
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- Comparative epigenome analysis using Infinium DNA methylation BeadChips.Briefings in bioinformatics · 2023Article
- Chimpanzee Extraversion scores vary with epigenetic modification of dopamine receptor gene D2 (Epigenetics · 2022Article
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- DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse.Cell genomics · 2022Article
- Arsenic Exposure, Blood DNA Methylation, and Cardiovascular Disease.Circulation research · 2022Article
- A mammalian methylation array for profiling methylation levels at conserved sequences.Nature communications · 2022Article
- Preclinical In Vivo Modeling of Pediatric Sarcoma-Promises and Limitations.Journal of clinical medicine · 2021Review
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- Age-associated epigenetic change in chimpanzees and humans.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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- Competitive repopulation of an empty microglial niche yields functionally distinct subsets of microglia-like cells.Nature communications · 2018Article
- Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray.PloS one · 2018Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse.
resultsIn silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10. Further annotation revealed that 85% of mEPIC probes overlapped with mm10.refSeq genes at different genomic features including promoters (TSS1500 and TSS200), 1st exons, 5'UTRs, 3'UTRs, CpG islands, shores, shelves, open seas and FANTOM5 enhancers. Hybridization of mouse samples to Infinium Human MethylationEPIC BeadChips showed successful measurement of mEPIC probes and reproducibility between inter-array biological replicates. Finally, we demonstrated the utility of mEPIC probes for data exploration such as hierarchical clustering.
conclusionsGiven the absence of cost and labor convenient genome-wide technologies in the murine system, our findings show that the Infinium MethylationEPIC BeadChip platform is suitable for investigation of the mouse methylome. Furthermore, we provide the "mEPICmanifest" with genomic features, available to users of Infinium Human MethylationEPIC arrays for mouse samples.
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