WGBS (Whole Genome Bisulfite Sequencing) and EM-seq (Enzymatic Methylation) Service

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Whole-genome bisulfite sequencing (WGBS) and Enzymatic Methylation (EM-seq) are the methods of choice for obtaining a comprehensive DNA methylation profiling, evaluating the methylation patterns of nearly every CpG site of the entire genome. By comparing the proportion of unconverted and converted cytosines at the same location, the methylation levels are determined with accuracy. Genome-wide methylation sequencing (WGBS and EM-seq) provides deep insights into gene regulation, allowing identification of novel epigenetic markers and targets for disease.

In-depth DNA methylation analysis

  • Very powerful solution for genome-wide biomarker discovery compatible with low input and highly fragmented cfDNA and FFPE samples
  • Single-nucleotide resolution
  • Evaluation of the methylation status of nearly every CpG sites of the entire genome
  • Detection of global methylation patterns including outside of CpG islands and in low-CpG-density regions
  • Identification of regions or even loci with differential methylation between groups using bioinformatics tools
  • Identification of methylation pattern/signature predictive and discriminating different groups with Data Mining approach
  • Providing a better understanding of development and disease

Comprehensive end-to-end service

  • From DNA QC to sequencing raw data
  • A dedicated scientist driving your project with high touch communication
  • High-quality bioinformatic support (on request) to assist you with data analysis

See our other DNA Methylation Profiling Services

  • Services Workflow

    WGBS Service includes:

    QC of the genomic DNA

    • Measurement of DNA concentration
    • Assessment of DNA quality

    Library Preparation


    • gDNA shearing on Bioruptor Pico (not necessary for cfDNA or FFPE)
    • Bisulfite conversion
    • Library preparation
    • QC of the WGBS libraries (DNA concentration, analysis of the profile)
    • gDNA shearing on Bioruptor Pico (not necessary for cfDNA or FFPE)
    • Library preparation with Enzymatic conversion
    • QC of EM-seq libraries (DNA concentration, analysis of the profile)

    Deep sequencing

    • Samples are sequenced on Illumina platform, paired-end reads of 150bp length (PE150)  
    • 400M raw reads on average per samples (when pooling 6 samples/lane)
    • Theoretical Coverage >30X for human, mouse and rat samples
    • Detection of >50 million CpGs with 6-9X average CpG coverage for human samples 
  • Bioinformatics Analysis



    • FASTQ raw data
    • FASTQC quality control insights
    • Alignment of bisulfite sequencing data against reference genome
    • Methylation calling and extraction
    • Summary statistics
    Differential methylation analysis
    • Methylation level analysis
    • Differentially methylated CpGs (DMCs) analysis
    • Differentially methylated regions (DMRs) analysis
    • Annotation of DMCs and DMRs for genomic regions (exons, introns, …) and for CpG island locations (islands, shores, shelves, ...)
    • Clustering analysis

    Gene ontology terms analysis

    • Enrichment analysis on gene associated with DMCs and DMRs
    • Get functional insights

    Pathway analysis

    • Identification of biological pathways in which genes associated with DMCs and DMRs may be over-represented (or under-represented)
    • Get mechanistic insights

    Data mining

    • Biomarker discovery
    • Determination of methylation pattern/signature that can be predictive and discriminate between different groups/conditions

  •  Documents
    Epigenomics Profiling Services FLYER
    Chromatin analysis DNA methylation services RNA-seq analysis
  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: WGBS (Whole Genome Bisulfite Sequencing) and EM-seq (Enzymatic Methylation) Service (Diagenode Cat# G02040000). Click here to copy to clipboard.

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    Development and epigenetic plasticity of murine Müller glia.
    Dvoriantchikova G, Seemungal RJ, Ivanov D
    The ability to regenerate the entire retina and restore lost sight after injury is found in some species and relies mostly on the epigenetic plasticity of Müller glia. To understand the role of mammalian Müller glia as a source of progenitors for retinal regeneration, we investigated changes in gene expres...

    The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue.
    Dvoriantchikova G, Seemungal RJ, Ivanov D
    The epigenetic plasticity of amphibian retinal pigment epithelium (RPE) allows them to regenerate the entire retina, a trait known to be absent in mammals. In this study, we investigated the epigenetic plasticity of adult murine RPE to identify possible mechanisms that prevent mammalian RPE from regenerating retinal...

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