Introduction

Whole Genome Bisulfite Sequencing (WGBS) is the gold-standard method for comprehensive genome-wide DNA methylation analysis at single-base resolution. By combining bisulfite conversion with next-generation sequencing (NGS), WGBS enables precise detection of methylated cytosines across the entire genome, providing an unbiased view of epigenetic modifications.

WGBS is widely used to investigate gene regulation, development, disease mechanisms, cancer epigenetics, and biomarker discovery, making it one of the most powerful tools for methylome research.

What is Whole Genome Bisulfite Sequencing?

DNA methylation is one of the most important epigenetic modifications, playing a central role in regulating gene expression, genomic stability, cellular differentiation, genomic imprinting, X-chromosome inactivation, and transposon silencing.

WGBS analyzes methylation across the entire genome, allowing researchers to identify methylated cytosines in CpG, CHG, and CHH contexts with single-nucleotide precision. Because it captures virtually all methylation events without prior target selection, WGBS provides the most comprehensive and unbiased methylation landscape available.

How WGBS Works

WGBS relies on bisulfite conversion, which selectively converts unmethylated cytosines into uracil while leaving methylated cytosines unchanged.

Following conversion:

• • DNA libraries are prepared for sequencing.

• • High-throughput sequencing generates genome-wide methylation data.
• • Bioinformatics analysis compares sequencing reads with the reference genome to identify methylated cytosines at single-base resolution.

• This workflow enables accurate quantification of DNA methylation throughout the genome.

Advantages of WGBS

• • Gold-standard method for genome-wide DNA methylation profiling
• • Single-base resolution across the entire genome
• • Comprehensive analysis of CpG, CHG, and CHH methylation
• • Unbiased detection without target enrichment
• • Suitable for humans, animals, and plants with reference genomes
• • Supports discovery of novel methylation biomarkers
• • High sensitivity and reproducibility
• • Ideal for large-scale epigenetic studies

Applications

• Gene Expression Regulation

Investigate how DNA methylation influences gene activation and silencing.

• Cancer Epigenetics

Identify methylation biomarkers and study epigenetic changes associated with tumor initiation, progression, and treatment response.

• Developmental Biology

Explore DNA methylation dynamics during embryonic development, stem cell differentiation, and cellular reprogramming.

• Disease Research

Examine methylation alterations linked to neurological, cardiovascular, metabolic, autoimmune, and other complex diseases.

• Environmental Epigenetics

Evaluate the impact of environmental factors, nutrition, and lifestyle on genome-wide methylation patterns.

• Evolutionary and Agricultural Research

Study epigenetic diversity, adaptation, breeding, and trait inheritance across plants and animals.

• Genome Stability and Imprinting

Investigate genomic imprinting, transposable element regulation, and mechanisms that maintain genome integrity.

DNA Methylation Detection Technologies

WGBS Workflow

Our optimized WGBS workflow delivers highly accurate and reproducible whole-genome methylation profiling.

• Genomic DNA extraction and quality assessment

• Bisulfite conversion of genomic DNA

• Library preparation and quality control

• High-throughput sequencing on Illumina platforms

• Bioinformatics analysis, including:

• - Quality control
• • Read alignment
• • Genome-wide methylation calling
• • Differentially methylated region (DMR) analysis
• • CpG island and promoter methylation analysis
• • Functional annotation and pathway enrichment
• • Comprehensive data visualization and publication-ready reports

DNA Methylation Microarray Services

N2Jenomics Lab Pvt. Ltd. offers advanced DNA methylation microarray services for high-throughput, genome-wide epigenetic profiling. Our microarray platforms enable accurate, reproducible, and cost-effective analysis of DNA methylation patterns, making them ideal for biomarker discovery, disease research, population studies, and clinical epigenetics.

We provide comprehensive solutions using the latest Illumina methylation arrays, supported by standardized laboratory workflows and expert bioinformatics analysis.

• Illumina Infinium MethylationEPIC v2.0 (935K)

The Illumina Infinium MethylationEPIC v2.0 BeadChip (935K) enables genome-wide analysis of approximately 935,000 CpG sites across the human genome.

Key Features

• - Genome-wide methylation profiling
• - Coverage of approximately 935,000 CpG loci
• - Single-CpG resolution
• - Enhanced genomic coverage over previous array versions
• - High reproducibility and analytical accuracy
• - Compatible with fresh, frozen, blood, saliva, and FFPE samples
• - Ideal for large-scale epigenetic and biomarker discovery studies

• Illumina Methylation Screening Array (MSA 270K)

The Illumina MSA 270K is designed for efficient methylation screening in large cohort studies and population-scale research.

Key Features

• - Approximately 270,000 methylation markers
• - High-throughput processing with up to 48 samples per array
• - Cost-effective solution for large studies
• - Excellent reproducibility and data quality
• - Suitable for disease association, aging, and environmental epigenetics research

WGBS Workflow

Our optimized Whole Genome Bisulfite Sequencing workflow ensures reliable and high-quality methylation profiling.

• DNA extraction and quality assessment

• Bisulfite conversion of genomic DNA

• Library preparation and Illumina adapter ligation

• High-throughput sequencing

• Comprehensive bioinformatics analysis

• Quality assessment and final reporting

Each step is performed under rigorous quality control to ensure accurate and reproducible results.

Sample Requirements

We support samples from a wide range of organisms, including:

• • Human
• • Animals
• • Plants
• • Microorganisms

Recommended Sample Types

High-quality DNA with minimal degradation is recommended for optimal sequencing performance.

Sequencing Specifications

• • Illumina high-throughput sequencing platforms
• • Paired-end 150 bp sequencing
• • ≥80% bases with Q30 or higher
• • Recommended sequencing depth of 20× or greater
• • Stringent quality control throughout the sequencing workflow

Bioinformatics Analysis

Our comprehensive bioinformatics pipeline includes:

• • Raw data quality assessment
• • Read alignment to the reference genome
• • Genome coverage and sequencing depth analysis
• • Cytosine methylation (mC) calling
• • Genome-wide methylation profiling
• • CpG methylation level analysis
• • Differentially Methylated Region (DMR) identification
• • DMR annotation
• • Gene Ontology (GO) enrichment analysis
• • KEGG pathway enrichment analysis
• • Clustering and comparative analysis
• • Publication-ready figures and comprehensive reports

Deliverables

Upon project completion, you will receive:

• • Raw sequencing data (FASTQ files)
• • Quality control reports
• • Processed methylation datasets
• • Bioinformatics analysis results
• • Differential methylation analysis (if applicable)
• • Functional enrichment analysis
• • Publication-quality visualizations
• • Comprehensive project report with interpretation

Why Choose N2Jenomics Lab Pvt. Ltd.?

• • Advanced Illumina sequencing platforms
• • Comprehensive DNA methylation solutions
• • Experienced genomics and bioinformatics experts
• • Rigorous quality control throughout the workflow
• • Customized analysis pipelines tailored to your research objectives
• • Fast turnaround times with dedicated technical support 

1. Which species are suitable for Whole Genome Bisulfite Sequencing?

WGBS can be applied to a wide range of eukaryotic organisms, including humans, animals, and plants. For optimal analysis, the species should have:

• • A well-assembled reference genome (preferably scaffold level or higher)

• • Comprehensive genome annotation
• • High-quality genomic DNA suitable for bisulfite conversion and sequencing

• A high-quality reference genome enables accurate read alignment, methylation calling, and downstream bioinformatics analysis.

2. What bioinformatics analyses are included in WGBS?

Our WGBS bioinformatics pipeline provides comprehensive methylation analysis, including:

• • Genome-wide methylation profiling
• • Cytosine methylation (CpG, CHG, and CHH) calling
• • Differentially Methylated Region (DMR) analysis
• • CpG island and promoter methylation analysis
• • Functional annotation and GO/KEGG pathway enrichment
• • Clustering and comparative methylation analysis
• • Correlation of DNA methylation with gene expression (when transcriptomic data are available)
• • Analysis of methylation patterns in genes, promoters, transposable elements, and other regulatory regions

These analyses provide valuable insights into epigenetic regulation and biological function.

3. What are the advantages of WGBS over other DNA methylation methods?

WGBS is considered the gold standard for DNA methylation analysis because it provides the most comprehensive and unbiased view of the methylome.

Key advantages include:

• • Genome-wide methylation profiling at single-base resolution
• • Detection of methylation across CpG, CHG, and CHH sequence contexts
• • Coverage of both CpG-rich and CpG-poor genomic regions
• • Absolute quantification of DNA methylation levels
• • Identification of novel methylation sites without prior target selection
• • Comprehensive analysis of promoters, enhancers, intergenic regions, and other regulatory elements

• Compared with MeDIP-Seq, WGBS provides base-level methylation information rather than relative enrichment. Compared with RRBS, WGBS offers complete genome coverage instead of focusing only on CpG-rich regions.

4. What are the limitations of WGBS?

Although WGBS is the most comprehensive DNA methylation sequencing method, several considerations should be taken into account:

• • DNA degradation: Bisulfite treatment can fragment DNA, making high-quality input DNA important.
• • Higher sequencing requirements: Whole-genome coverage requires greater sequencing depth, resulting in higher costs and larger data volumes.
• • Library preparation complexity: Efficient bisulfite conversion and library preparation are essential for accurate methylation analysis.
• • Limited modification discrimination: Conventional WGBS accurately detects 5-methylcytosine (5mC) but cannot reliably distinguish it from 5-hydroxymethylcytosine (5hmC) without additional specialized assays.