Please select your location below for region-specific information.
Americas

(North America, South America, and the Caribbean)

Asia-Pacific

(Including Hong Kong SAR, Macau SAR, and Taiwan)

EuropeMainland China
EuropeMainland China
Middle-East & AfricaJapan
JapanKorea
KoreaMiddle-East & Africa
Power your research with expert solutions and reliable results.
Services

Whole Genome Methylation Sequencing

Introduction to Whole Genome Methylation Sequencing

Whole genome methylation sequencing enables researchers to investigate important epigenetic modifications, such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), which play key roles in gene regulation, development and genomic stability. Novogene offers a range of solutions to detect whole genome methylation tailored to your research needs:

1. Whole Genome Bisulfite Sequencing (WGBS) – The Gold Standard:

WGBS remains the gold standard for detecting cytosine methylation at single-nucleotide resolution. Despite its effectiveness, bisulfite treatment can cause DNA damage and bias. Novogene’s WGBS service is optimized to minimize these effects, delivering reliable, high-quality data for your research needs.

2. Enzymatic Methyl Sequencing:

To address the limitations of bisulfite treatment, Novogene offers Enzymatic Methyl-seq, which uses enzyme-based conversion under milder conditions. This approach preserves DNA integrity, reduces damage and produces high-quality libraries, making it suitable for diverse sample types including genomic DNA, formalin-fixed paraffin-embedded (FFPE) DNA, and cell-free (cf) DNA.

3. PacBio Long-Read Sequencing:

Novogene’s PacBio long-read sequencing service provides an advanced option for comprehensive methylation profiling, capturing full-length methylated regions and directly detecting modifications without bisulfite conversion. This solution offers unparalleled insights into complex methylation landscapes and structural variations. Additionally, it can also detect DNA methylation in microbial genomes.

4. Oxford Nanopore Technology Long-Read Sequencing:

Our Nanopore sequencing service enables direct, real-time methylation detection in long DNA fragments, providing a clear view of methylation patterns and structural variations without the biases of traditional methods. This technology is ideal for complex epigenetic analysis. Nanopore also allows the possibility of directly detecting RNA modifications. Additionally, it can also detect DNA methylation in microbes.

Novogene has experience with WGBS, enzymatic methyl sequencing as well as long read sequencing across a diverse range of species. We provide end-to-end services that include library preparation, delivery of high-quality sequencing data and bioinformatics support to analyze methylation pattern across the genome.

Applications of Whole Genome Methylation Sequencing

Whole Genome Methylation sequencing has several applications, including:

  • Profiling methylation patterns at CG, CHG and CHH sites with single nucleotide resolution
  • Identifying differentially methylated sites associated with diseases, experimental treatments or differing sample conditions
  • Understanding mechanisms of cell differentiation or tissue development based on methylation profiles
  • Investigating gene expression and silencing mechanisms

Benefits of  Novogene’s Whole Genome Methylation Sequencing service

  • Extensive Experience: Novogene has experience working with whole genome bisulfite sequencing, enzymatic methyl sequencing, as well as methylation detection using long read sequencing across a diverse range of sample types.
  • High-Quality Data: We deliver high-quality sequencing data that meets leading industry standards.
  • Bioinformatics Support: We provide comprehensive bioinformatics support, including DMR (differentially methylated region) and DMP (differentially methylated position) analysis, complete with ‘publication ready’ figures. We also offer analysis options for joint profiling of epigenome and transcriptome data.
  • Latest platforms: We provide whole genome methylation sequencing on Novaseq X Plus, which is the latest Illumina platform providing exceptional throughput. Additionally, we also provide the option of direct methylation detection on the latest platforms from PacBio (Revio) as well as Oxford Nanopore Technologies (PromethION).
  • Fast turnaround times: Our sequencing labs are located near you, in Germany and the UK, allowing for reduced shipping times. With our large sequencing capacity and automated and streamlined workflows, we ensure that you receive your data promptly without compromising on quality. 
  • Customer Service System (CSS): Novogene’s Customer Self Service System (CSS) is an online project management portal that streamlines project management and provides direct access to all your sequencing projects in one place. You can view your sequencing project(s), track their progress, access reports, collaborate with your team members and obtain other useful information at one place.

Epigenetic Sequencing Service Flyer

DNA methylation is an epigenetic mechanism that occurs by the addition of a methyl group to cytosine nucleotides in DNA. This modification often alters the function and expression of the affected genes. Whole genome bisulfite sequencing (WGBS) is used to convert non-methylated cytosines to uracil, leaving the methylated cytosines to be identified by sequencing on a genome-wide scale. IP-seq is used to study the interaction between proteins and nucleic acids by sequencing the protein-binding motifs within DNA and RNA.

Download the Service Flyer

On-demand Webinar

A Beginner’s Guide to Next Generation Sequencing Solutions for Epigenetics Research

In this webinar, we will showcase Novogene’s diverse sequencing solutions for epigenetics research, including techniques to detect DNA methylation such as Whole Genome Bisulphite Sequencing and EM-seq, determining chromatin accessibility using ATAC-seq, and studying histone modifications (e.g., ChIP-seq), among others. We will delve into the underlying principles of these technologies, explore their various applications, and outline the workflows and analysis pipelines used to achieve comprehensive epigenetic insights.

We will talk about myriad microbial sequencing options such as microbial whole genome sequencing, metagenomics, and metatranscriptomics. We will also discuss recent advances in the field such as the applications of long-read sequencing and highlight Novogene’s diverse microbial sequencing solutions to aid your research.

Learning Objectives:

  • Discover sequencing solutions tailored for epigenetics research
  • Understand the principles and applications of the various NGS solutions for epigenetics research
  • Gain insight into the workflows and bioinformatics analysis pipelines of Novogene’s epigenetics solutions.

Watch Now

Whole Genome Methylation Sequencing Specifications: DNA Sample Requirements

Sample Type Required Amount Concentration Purity
Genomic/FFPE DNA* ≥ 100 ng ≥5 ng/μL 0＜OD260/230＜3;
no degradation, no contamination
cfDNA/ctDNA* ≥20 ng ≥3 ng/μL 0＜OD260/230＜3;
No EDTA in solvent

Note: Sample amounts are listed for Illumina sequencing and are for reference only. Please don’t hesitate to reach out to us for detailed information or customized requests.
*FFPE: Formalin-Fixed, Paraffin-Embedded; cell-free DNA, circulating-tumor DNA

Whole Genome Methylation Sequencing Specifications: Sequencing and Analysis

Sequencing Platform Illumina NovaSeq X Plus
Read Length Paired end 150 bp
Recommended sequencing depth ≥ 30× coverage for species with reference genome
Standard Data Analysis
  • Data 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)
    		•

    Note: Sequencing parameters and analysis contents displayed are only for reference. Please contact us for detailed information as well as information on long read sequencing options.

    Project Workflow of Novogene’s Whole Genome Methylation Sequencing Service

    Novogene’s Whole Genome Methylation Sequencing service comprises several steps, including sample QC, sample processing, DNA library preparation, Illumina PE150 sequencing and data analysis using bioinformatics pipelines. From DNA sampling to sequencing library preparation, every step can potentially impact the quality and quantity of data output, directly influencing the results of the subsequent bioinformatics analysis. Novogene performs rigorous checks at every stage, including sample quality control, library quality control and sequencing data quality control, to ensure the highest quality, accuracy and reliability of the sequencing data delivered to our customers. Novogene also offers methylation and other DNA/RNA modification profiling using long read technologies such as PacBio and ONT.

    Featured Publications using Novogene WGBS Service

    Whole Genome Bisulfite Sequencing (WGBS) is a powerful method to identify individually methylated cytosines on a genome-wide scale. The deep reach of the methylome (including methylated cytosine detection), the promoter detection of differentially methylated sites and regions, and related functional analysis of the Differentially Methylated Region (DMR) and Differentially Methylated Promoter (DMP), are all essential for understanding gene expression and other processes that are subject to epigenetic regulation. Here summarizes a list of publications that used Novogene WGBS service.

    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)

    RNA Immunoprecipitation Sequencing (RIP-seq)

    Chromatin Immunoprecipitation Sequencing (ChIP-seq)