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Services

Direct Methylation Sequencing (DMSeq)

Introduction to Direct Methylation Sequencing (DMSeq)

DNA methylation at cytosine (5mC) is a key epigenetic modification that regulates gene expression, chromatin structure, and genome stability. Dysregulated methylation drives tumorigenesis, neurodegenerative diseases, and complex disorders. Direct Methylation Sequencing (DMSeq) is a bisulfitefree, enzymatic methylsequencing technology that detects 5mC at singlebase resolution. It preserves DNA integrity, avoids harsh chemical damage, and enables accurate profiling even with lowinput or degraded samples.

Novogene offers flexible DMSeq solutions tailored to your research needs:

  • Illumina 5base chemistry: Targets 5mC only, delivering clean, precise methylation calls ideal for standard epigenetics and SNVcodetection studies.
  • Watchmaker TAPS+ chemistry: Captures both 5mC and 5hmC, providing a comprehensive view of active epigenetic landscapes for neuroscience, development, and cancer research.

Applications of Direct Methylation Sequencing (DMSeq)

Novogene delivers highquality, publicationready DMSeq data and analysis, supporting a broad range of epigenetic research:

  • Single‑base resolution profiling of 5mC (5‑base) or combined 5mC+5hmC (TAPS+) across the whole genome
  • Identification of differentially methylated regions (DMRs) linked to development, disease, or experimental conditions
  • Deciphering epigenetic mechanisms in cell differentiation, tissue development, and embryogenesis
  • Integrated analysis of methylation with genetic variations (SNV) for multi‑omics insights
  • Biomarker discovery for cancer, neurological disorders, and aging‑related diseases
  • High‑quality methylome profiling from low‑input or degraded samples (e.g., cfDNA, FFPE)

Benefits of Novogene DM-Seq Service?

  • Flexible chemistry options：Both 5‑base (5mC) and TAPS+ (5mC+5hmC) are available to meet different research goals.
  • Customizable sequencing depth：10 Gb / 30 Gb / 90 Gb / 150 Gb or any desired data output can be tailored.
  • Broad sample compatibility：Supports gDNA, FFPE, and cfDNA for diverse research scenarios.
  • Fast end‑to‑end turnaround：Project delivery within 4–8 weeks ensures efficient research progress.

DM-Seq Specifications: DNA Sample Requirements

Service Sample Type Amount (Qubit®) Volume Concentration Purity or fragment size
(NanoDrop™/Agarose Gel)/Sample Status
Direct Methylation Sequencing (DM‑Seq) Genomic DNA ≥ 40 ng ≥ 20 μL ≥ 2 ng/μL 1.8 ＜OD260/230＜ 2.0;

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

DM-Seq Specifications: Sequencing and Analysis

Platform Type Illumina NovaSeq XPlus
Read Length Paired-end 150 bp
Sequencing Depth ≥ 30× coverage for the species with reference genome
Standard Data Analysis Data Quality Control (QC)

1. Sequencing Data Quality Assessment:

1) Remove adapters, contaminant sequences, and low-quality read pairs;

2) Summarize sequencing output;

3) Calculate error rate, quality scores, and GC content

Data Alignment

1. Alignment and Filtering:

1) Align reads to the reference genome;

2) Remove PCR/sequencing duplicates;

3) Summarize sequencing depth and coverage

Methylation Site Detection and Analysis

1. Methylation site detection (mC calling)

2. Single-sample methylation analysis

3. Sample correlation analysis

4. Combined analysis of methylation levels across comparison groups

5. Differentially Methylated Region (DMR) analysis

Variant Analysis

1. SNP detection and annotation

2. InDel detection and annotation

3. Structural Variant (SV) detection and annotation

4. Copy Number Variant (CNV) detection and annotation summary

Note: Sequencing parameters and analysis contents displayed are only for reference. Download the Service Specifications to learn more. For detailed information, please contact us with your customized requests.

Project Workflow of Novogene DM‑Seq Service

The Novogene DM‑Seq service is comprised of four steps. Sample preparation is followed by library preparation, sequencing and bioinformatics analysis. To construct a methylation library, enzymatic methylation conversion is performed initially, without sodium bisulfite treatment, enabling direct detection of methylated cytosines. Libraries are then sequenced using Illumina PE150 and the reads are processed with bioinformatics pipelines.

In order to ensure the accuracy and reliability of sequencing data, Novogene audits every experimental step strictly by quality control and ensures high-quality data output fundamentally, from DNA sampling to obtaining the final data report. Obtaining high-quality data is the premise to ensure that bioinformatics analysis is correct, comprehensive and credible.





Distribution of Genome Coverage

Novogene WGBS Distribution of Genome Coverage

Methylation Level Distribution on Whole Genome

Novogene WGBS Methylation Level Distribution on Whole Genome

Heatmap Analysis for Methylation Levels of Gene Functional Region

Novogene WGBS Heatmap Analysis for Methylation Levels of Gene Functional Region

Methylation Level Distribution at Functional Genetic Elements

Novogene WGBS Methylation Level Distribution at Functional Genetic Elements

Circos Plot for DMR Condition in three contexts (CG, CHG, CHH)

Novogene WGBS Circos Plot for DMR Condition in three contexts (CG, CHG, CHH)

Diagram of GO Enrichment

Novogene WGBS GO Enrichment

More Research Services

Reduced Representation Bisulfite Sequencing (RRBS)

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing)

RNA Immunoprecipitation Sequencing (RIP-seq)

Chromatin Immunoprecipitation Sequencing (ChIP-seq)

Whole Genome Bisulfite Sequencing (WGBS)

Enzymatic Methyl Sequencing