Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

被引:1
|
作者
Meyer, Olivia Strunge [1 ]
Andersen, Mikkel Meyer [1 ,2 ]
Borsting, Claus [1 ]
Morling, Niels [1 ,2 ]
Wulf, Hans Christian [3 ]
Philipsen, Peter Alshede [3 ]
Lerche, Catharina Margrethe [3 ,4 ]
Andersen, Jeppe Dyrberg [1 ]
机构
[1] Univ Copenhagen, Fac Hlth & Med Sci, Dept Forens Med, Sect Forens Genet, Frederik Vs Vej 11, DK-2100 Copenhagen, Denmark
[2] Aalborg Univ, Dept Math Sci, DK-9220 Aalborg, Denmark
[3] Copenhagen Univ Hosp Bispebjerg & Frederiksberg, Dept Dermatol, DK-2400 Copenhagen, Denmark
[4] Univ Copenhagen, Dept Pharm, DK-2100 Copenhagen, Denmark
关键词
Whole genome bisulphite sequencing; Infinium Mouse Methylation BeadChip; DNA methylation; epidermis; hairless mice; CpG methylation;
D O I
10.1080/15592294.2022.2144574
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory.
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页数:10
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