Genome-Wide DNA Methylation Analysis with Sequencing and Array Options
DNA methylation is a central mechanism of epigenetic regulation, influencing gene expression, genomic imprinting, and chromatin organization. Selecting the right analytical approach — sequencing-based or array-based, whole-genome or targeted, short-read or long-read — depends on your research question, sample type, and throughput requirements. CD Genomics provides a full spectrum of genome-wide DNA methylation analysis services across multiple platforms and methods.
We offer a comprehensive range of sequencing-based methylation analysis methods — from whole-genome to targeted, short-read to long-read, and bisulfite to bisulfite-free — each optimized for specific research needs and sample types.
Whole Genome Bisulfite Sequencing (WGBS)
Single-base resolution across ~28–36 million CpG sites. Sodium bisulfite conversion enables gold-standard genome-wide 5mC profiling for comprehensive methylome discovery.
Best for: Full methylome characterization, biomarker discovery, non-model organisms.
Antibody-based enrichment of methylated DNA fragments without bisulfite conversion. Region-based resolution suitable for genome-wide methylation scanning.
Best for: Large-sample screening, regional methylation pattern studies.
Nanopore-based direct detection of 5mC from native DNA without bisulfite or PCR. Resolves methylation in repetitive regions and segmental duplications.
Best for: Repeat-rich genomes, SV-methylation co-analysis, haplotype phasing.
Enzymatic 5mC→T conversion for dual detection of methylation and genetic variation (SNV/Indel/CNV/SV) from a single library. Works with 1 ng cfDNA or 50 ng gDNA.
Best for: Low-input samples (cfDNA, FFPE), dual-omic analysis, allele-specific methylation.
SMRT sequencing or enrichment-based N6-methyladenine (6mA) detection across the genome. Targets non-CG DNA modifications in prokaryotic and eukaryotic genomes.
Best for: Prokaryotic epigenetics, plant DNA methylation, non-CG modification research.
Methylation-sensitive restriction enzyme digestion combined with sequencing. Pairs with MeDIP-seq (M&M strategy) for complementary methylation profiles at reduced cost.
Hybrid-capture enrichment of CpG islands and promoter regions. High-depth analysis of ~2 million CpG sites in functionally critical regions for human and mouse.
Illumina Infinium methylation arrays provide cost-effective, high-throughput methylation profiling at predefined CpG sites. We offer three array options:
The Infinium Mouse Methylation BeadChip covers >285,000 CpG sites across the mouse genome. We also offer mouse-specific CpG island microarray services for targeted analyses.
Not sure which modification analysis fits your research? Share your sample type and study goals with us, and our epigenetics specialists will recommend the most suitable approach.Get Expert Advice
Sample
Sample Requirements at a Glance
Sample quality and quantity directly affect data quality. Guidelines below are general references — share your sample type and project goals for a personalized assessment.
Service
DNA Input (Recommended)
Concentration
Key QC Points
WGBS
≥1 μg gDNA (min 200 ng)
≥10 ng/µL
OD260/280: 1.8–2.0; DNA integrity by gel
RRBS
≥1 μg gDNA (min 20 ng)
≥20 ng/µL
MspI digestion efficiency verified
MeDIP-seq
≥2 μg gDNA (min 1 μg)
≥20 ng/µL
Enrichment efficiency by qPCR
5-Base Sequencing
50–100 ng gDNA / 1–20 ng cfDNA
≥10 ng/µL
cfDNA: 166 bp peak; FFPE: DV200 >30%
Long-Read Methylation
≥1 μg high-MW gDNA
≥20 ng/µL
Fragment size >15 kb; no shearing
Methylation Array (Human)
250–500 ng gDNA
≥25 ng/µL
Bisulfite conversion efficiency ≥99%
Methylation Array (Mouse)
250–500 ng gDNA
≥25 ng/µL
Bisulfite conversion efficiency ≥99%
This is a reference summary. Share your sample type, quantity, and research purpose with us, and we will help determine the most suitable method and sequencing strategy for your project.Send Your Sample Information
Workflow
Workflow: From Sample to Methylation Data
The general workflow follows a standardized pipeline with method-specific variations at the conversion step.
Sample QC and DNA Extraction — QC: DNA quantity (Qubit), purity (OD260/280), integrity (gel or Fragment Analyzer). cfDNA: ~166 bp peak. FFPE: DV200 assessed.
DNA Conversion or Enrichment — Bisulfite conversion (WGBS/RRBS), enzymatic conversion (5-base), antibody enrichment (MeDIP), or direct detection (Nanopore/arrays). QC: conversion efficiency ≥99%.
Library Construction — End repair, adaptor ligation, PCR amplification with unique molecular indexes. QC: library yield and size distribution.
Sequencing or Array Scanning — Illumina NovaSeq 6000/NovaSeq X or iScan. QC: Q30 ≥ 85%, call rate for arrays.
DNA methylation analysis services are supported by multiple sequencing and array platforms. The choice of platform depends on the method, throughput requirements, and desired data type.
Platform
Application
Used For
Illumina NovaSeq 6000 / NovaSeq X
High-throughput short-read sequencing
WGBS, RRBS, MeDIP-seq, 5-base sequencing, CpG island panel sequencing
Direct 5mC detection, repeat-region methylation analysis
PacBio Sequel II / Revio
SMRT long-read sequencing
DNA 6mA detection, native base modification analysis
Qubit / Fragment Analyzer / Bioanalyzer
QC instrumentation
DNA quantification and integrity assessment across all methods
For targeted enrichment applications, we use hybrid-capture systems compatible with both bisulfite-converted and native DNA libraries.
Bioinformatics
Bioinformatics Analysis and Deliverables
DNA methylation data analysis is structured to support publication-ready results. All services include the following core deliverables and analysis modules.
Standard Deliverables per Sample: Raw FASTQ (or IDAT for arrays), QC report, aligned data (BAM), methylation calls (beta values or methylation level matrices), data summary report (PDF).
Below are representative examples of DNA methylation data analysis outputs from our service. Actual results vary by method, sample quality, and sequencing depth.
Whole-Genome Circos Plot — Circular genome visualization showing chromosome-wide methylation density and distribution.
CpG Island & Feature Methylation — Lollipop diagrams and violin plots for CpG-level methylation across promoters, gene bodies, and intergenic regions.
Beta-Value Density & Clustering — Distribution curves and MDS scatter plots for cohort-level sample comparison and group separation.
Applications
Applications of DNA Methylation Analysis
Cancer Epigenetics
DNA methylation profiling identifies tumor suppressor silencing, oncogene hypomethylation, and cancer-type-specific methylation signatures. Applications include liquid biopsy biomarker development, tumor subtyping, and treatment response monitoring.
Aging and Longevity
Epigenetic clocks based on age-associated CpG methylation changes enable biological age estimation, healthspan assessment, and intervention evaluation.
Environmental Epigenetics
Characterizes methylation changes induced by environmental exposures (pollutants, diet, stress) and their transgenerational inheritance.
Developmental Biology
DNA methylation dynamics during embryogenesis, cell differentiation, and tissue specification are central to understanding developmental programming.
Population-Scale EWAS
Epigenome-wide association studies with thousands of samples benefit from the cost-efficiency of methylation arrays or RRBS.
Non-Model Organism Research
Methylation profiling in agricultural species, evolutionary biology, and ecology, with reference-free analysis where needed.
Method Comparison
How to Choose the Right Method
There is no single best approach — the optimal method depends on your research question, sample type, throughput, and budget.
Dimension
WGBS
RRBS
MeDIP-seq
5-Base
Long-Read (ONT)
Array (EPIC)
Resolution
Single-base
Single-base
Region-based
Single-base
Single-base
Single-base (targeted)
CpG Coverage
~28M
~3–7M
Enriched peaks
~28M
Unique in repeats
~935K targeted
DNA Input
200 ng–1 μg
20 ng–1 μg
1–2 μg
1 ng–100 ng
≥1 μg (HMW)
250–500 ng
Bisulfite-Free
No
No
Yes
Yes (enzymatic)
Yes (direct)
No
Variant Detection
Limited
Limited
No
SNV/Indel/CNV/SV
SNV/SV
No
Best For
Full methylome discovery
CpG-rich regions
Large-scale screening
Low-input dual-omics
Repetitive regions
Large cohort EWAS
Start with your sample — Limited DNA? Prioritize 5-base or arrays. High-MW gDNA with repeat concerns? Consider long-read. Match resolution to question — Discovery needs WGBS/5-base. CpG islands need RRBS or panels. Consider throughput — Large cohorts benefit from arrays or RRBS. Single-sample discovery needs WGBS/5-base. Need dual-omic data? — 5-base sequencing is the only single-assay solution for methylation + variant co-detection.
Reviews
What Our Clients Say
"The DNA methylation analysis services have been instrumental in our cancer epigenetics research. Having access to both WGBS and array options under one service team made it straightforward to match methods to different phases of our study — discovery with WGBS, validation with arrays. The bioinformatics support was particularly helpful for interpreting the large datasets."
— Principal Investigator, Cancer Epigenetics Lab, Academic Medical Center
"We use RRBS routinely for our environmental epigenetics cohort studies — hundreds of samples per project. The consistency of data across batches and the detailed QC reporting give us confidence in our cross-study comparisons. The double RRBS protocol has noticeably improved CpG coverage in promoter regions."
— Associate Professor, Environmental Health Sciences, Research University
"We needed long-read methylation analysis for a repeat-rich plant genome, and the Nanopore service delivered data that short-read bisulfite sequencing could not map. The technical team helped optimize the DNA extraction to meet the high-MW requirement, and the final data quality exceeded our expectations."
— Research Group Leader, Plant Epigenetics, Agricultural Research Institute
Publications
Publications
The following publications cite DNA methylation analysis services provided by CD Genomics, demonstrating the application of our services across diverse research areas.
For Research Use Only. Not for use in diagnostic procedures. CD Genomics provides DNA methylation analysis services exclusively for research purposes. Service parameters, platform availability, and bioinformatics analysis modules are subject to project-specific optimization. The mention of third-party trademarks (Illumina, NovaSeq, Infinium, Oxford Nanopore, PacBio) is for informational purposes only.
