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Enzymatic Methyl Sequencing (EM-Seq)

Genome-wide, single-base resolution profiling of DNA methylation to reveal epigenetic regulation and genome-wide methylation patterns.

DNA methylation at the C5 position of cytosine plays a crucial role in gene expression and chromatin remodelling. As one of the most important research areas in epigenetics, methyl-seq tech is .With the development of high-throughput sequencing technology, WGBS has gradually become the gold standard for DNA methylation sequencing.


Enzymatic Methyl Sequencing has been developed to overcome the shortcomings of WGBS, an enzyme-based method for the detection of 5mC and 5hmC at the single base level. The enzymatic conversion method is gentler and causes less DNA damage, thereby avoiding DNA molecule cleavage and loss.

Benefits of EM-Seq

Enhanced Data Quality & Coverage
Enhanced Data Quality & Coverage

EM-Seq (Enzymatic Methyl-seq) achieves uniform genome-wide coverage with minimal DNA damage, providing higher mapping rates and more consistent methylation calls—especially in GC-rich and difficult-to-sequence regions.


Low-Input & Degraded Sample Compatibility
Low-Input & Degraded Sample Compatibility

The enzyme-based conversion preserves DNA integrity, enabling robust methylation profiling from ultra-low input, FFPE, and other degraded sample types where bisulfite methods may fail.

Multi-Context Methylation Detection
Multi-Context Methylation Detection

Using validated enzymatic and bioinformatic pipelines, we accurately quantify methylation at single-base resolution in CG, CHG, and CHH contexts across a broad range of species.


Rapid Turnaround & Scalable Capacity
Rapid Turnaround & Scalable Capacity

Leveraging automated library preparation and high-throughput sequencing platforms, we deliver high-quality EM-Seq data with industry-leading speed and scalability for both small studies and large cohorts.

Applications

Novogene delivers high-quality data and publication-ready analysis results of EM-Seq (Enzymatic Methyl-seq) services, to facilitate advanced epigenetic research with enhanced coverage and reduced DNA damage:

High-Resolution Methylation Profiling

Accurately quantify methylation levels at single-base resolution across CG, CHG, and CHH contexts, with improved coverage in challenging genomic regions.


Sensitive Differential Methylation Detection

Identify differentially methylated sites (DMS) and regions (DMRs) between experimental groups with higher sensitivity and reproducibility, enabled by uniform genomic coverage.

Enhanced Mechanistic Insights

Uncover regulatory roles of DNA methylation in gene expression, cell differentiation, and developmental processes through integrative analysis of methylation and transcriptomic data.

Biomarker Discovery for Disease Research

Detect subtle methylation changes associated with diseases, including cancer, neurological disorders, and aging, supporting early detection and mechanistic studies.

Multi-Sample Comparative Epigenomics

Perform systematic comparison of methylation patterns across tissues, treatments, or timepoints to reveal dynamic epigenetic regulation in development and disease.

Functional Annotation & Pathway Analysis

Annotate DMRs to genomic features (promoters, enhancers, gene bodies) and perform enrichment analysis to link methylation changes to biological pathways and functions.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample TypeAmountPurity or fragment size
Genomic DNA≥ 50 ngFragments are above 5000 bp, and mainly above 13000 bp, no degradation, no contamination, no EDTA
cfDNA≥ 50 ngAgilent 2100 peak at 170bp and integer multiples, no genomic contamination, no contamination, no EDTA

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Platform TypeIllumina NovaSeq platform
Read LengthPaired-end 150 bp
Sequencing Depth≥ 20× coverage for the species with reference genome
Standard Data AnalysisData Quality Control
mCs detection, methylation level calculation
Methylation level and frequency distribution
Differentially Methylated Site (DMS) detection
Differentially Methylated Regions (DMRs), Differentially Methylated Promoter (DMPs) detection and annotation
Function enrichment of DMR-associated genes and DMP-associated genes
Visualization of BS seq data
Comparative analysis (among samples)
Co-Analysis with mRNA-seq (Integrated Analysis of Methylome and Transcriptome)The distribution of gene methylation level and expression level at the chromosome level, and the distribution of methylation level and expression level at the upstream and downstream levels of genes.
The relationship between DMR related gene’s expression and methylation modification
The intersection of DMR related genes and differentially expressed genes, and display the methylation level, expression amount and annotation information of the intersection genes in different forms.
Functional analysis of DMR related genes and differentially expressed genes, including GO, KEGG, and Motif Analysis.

Project Workflow of Novogene enzymatic methylation sequencing Service

The Novogene enzymatic methylation sequencing service comprises four steps: Sample preparation, library preparation, sequencing, and bioinformatics analysis, DNA extraction service is also available. The enzymatic methylation sequencing conversion reaction is a two-step process: 1) TET2 and T4-BGT Protection of 5mC and 5hmC. 2) APOBEC then deaminates cytosines into uracils. Please contact us for more information about your enzymatic methylation sequencing projects.


To guarantee the accuracy and reliability of sequencing data, Novogene audits every experimental step through quality control, fundamentally ensuring high-quality data output from sampling to the final data report. This commitment to high-quality data is essential for the correctness, comprehensiveness, and credibility of bioinformatics analysis.

Project Workflow of Novogene enzymatic methylation sequencing Service

Resources

Demo Results

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Distribution of Genome Coverage
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Methylation Level Distribution on Whole Genome
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Heatmap Analysis for Methylation Levels of Gene Functional Region
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Methylation Level Distribution at Functional Genetic Elements
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Circos Plot for DMR Condition in three contexts (CG, CHG, CHH)
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Diagram of GO Enrichment

Webinars

Novogene’s Comprehensive Methylation Service WGBS, EM-seq, and mRNA-WGBS Analysis

This webinar will provide you with a comprehensive overview of whole genome methylation sequencing services at Novogene, including Whole Genome Bisulfite Sequencing (WGBS), Enzymatic methyl sequencing (EM-seq), and mRNA-WGBS associated analysis.

(Novogene’s Comprehensive Methylation Service WGBS, EM-seq, and mRNA-WGBS Analysis)
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