Directed Methylation Sequencing (DM-Seq)

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. Directed Methylation Sequencing (DM-Seq) is a bisulfite free, enzymatic methyl sequencing technology that detects 5mC at single base resolution. It preserves DNA integrity, avoids harsh chemical damage, and enables accurate profiling even with low input or degraded samples.

Novogene offers flexible DM-Seq solutions tailored to your research needs:

• Illumina 5 base chemistry: Targets 5mC only, delivering clean, precise methylation calls ideal for standard epigenetics and SNV co detection studies.

• Watchmaker TAPS+ chemistry: Captures both 5mC and 5hmC, providing a comprehensive view of active epigenetic landscapes for neuroscience, development, and cancer research.

Benefits

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.

Applications

Novogene delivers high quality, publication ready DM-Seq data and analysis, supporting a broad range of epigenetic research.

Core Technical Strengths

• Single base resolution profiling of 5mC (5 base) or combined 5mC+5hmC (TAPS+) across the whole genome

• High quality methylome profiling from low input or degraded samples (e.g., cfDNA, FFPE)

Main Research & Application Scenarios

• 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

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.

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

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.

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

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.

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

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.

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

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

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.

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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.

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

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.

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

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.

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

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.

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

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq Service

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 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: 2. Remove adapters, contaminant sequences, and low-quality read pairs; 3. Summarize sequencing output; 4. Calculate error rate, quality scores, and GC content Data Alignment 1. Alignment and Filtering: 2. Align reads to the reference genome; 3. Remove PCR/sequencing duplicates; 4. 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

Project Workflow of Novogene DM-Seq 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

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