Epigenomics Services

Epigenomics Sequencing, Profiling & Analysis Services

Support complex epigenomics studies from assay selection to data interpretation across DNA and RNA modifications, cfDNA, chromatin regulation, and 3D genome organization.

Study‑Driven Design Methods matched to research goals, samples, and study scale

Flexible Sample Support Tissue · Cells · Blood · cfDNA · FFPE · DNA · RNA

Complementary Platforms NGS · Long‑read · Microarray · LC–MS/MS

Integrated Analysis Assay‑specific QC · Bioinformatics · Multi‑layer analysis

Explore Epigenomics Services Discuss Your Project

Epigenomics sequencing and profiling research

Supporting Research Published in Leading Journals

Our epigenomics services have supported client studies published in Nature Communications, Nature Cancer, Science Advances, and other peer-reviewed journals.

DNA Methylation · Chromatin Regulation · RNA Modification · Integrated Epigenomics

Explore Client Research

Supporting Diverse Samples and Research Applications

Support epigenomics research across diverse sample types, biological systems, and study areas with flexible workflows tailored to your project needs.

Tissues · Cells · Blood · Plasma & cfDNA · FFPE · Genomic DNA · RNA
Cancer · Aging · Development · Disease Research · Biomarker Discovery · Drug Discovery

Explore Our Research Capabilities

Diverse biological samples for epigenomics research

Epigenetic Clock Analysis for Biological Age Research

Explore age-associated DNA methylation patterns with epigenetic clock analysis for aging, development, intervention, and comparative research.

DNA Methylation · Epigenetic Age Estimation · Clock Model Selection · Comparative Analysis
Human · Animal · Multi-Cohort Studies

Explore Epigenetic Clock Analysis

Epigenetic clock analysis for biological aging

Trusted by Researchers at Leading Institutions

Researchers from universities, research institutes, government agencies, and biotechnology organizations worldwide have used our services to support their research.

Singapore Institute for Clinical Sciences

Explore Epigenomics by Research Goal

Start with the Biological Question

Explore epigenomics sequencing, profiling, and analysis approaches based on your biological question, from DNA methylation and RNA modification to chromatin regulation, molecular interactions, 3D genome organization, and integrated analysis.

DNA and cell‑free DNA methylation research

DNA & cfDNA Modifications

Profile DNA methylation and related modifications using genome-wide, targeted, low-input, and cfDNA methylation sequencing and profiling approaches.

WGBS · EM‑seq · RRBS · Methylation Arrays · Targeted Profiling · 5mC / 5hmC

Explore DNA Modifications Explore cfDNA Modifications

RNA modification and regulatory research

RNA Modifications

Investigate RNA methylation, other RNA modifications, and epitranscriptomic regulation across coding and non-coding RNA.

MeRIP‑seq · GLORI‑seq · m6A · m6Am · m5C · Ψ · tRNA · GlycoRNA

Explore RNA Modification Services

Chromatin Regulation

Characterize chromatin accessibility, histone modifications, and transcription factor binding.

ATAC‑seq · ChIP‑seq · CUT&RUN · CUT&Tag · DAP‑seq

Explore Chromatin Profiling

RNA protein DNA and chromatin interaction research

Molecular Interactions

Study interactions among RNA, proteins, DNA, and chromatin to investigate regulatory relationships.

RIP‑based Assays · CLIP‑based Assays · ChIRP · R‑loop Profiling · DRIPc‑seq

Explore Molecular Interaction Analysis

Three‑dimensional genome organization research

3D Genome Organization

Map chromatin contacts and genome architecture for 3D genome analysis, from genome-wide interactions to selected regulatory regions.

Hi‑C · Capture Hi‑C · Promoter Capture Hi‑C · Micro‑C · HiChIP

Explore 3D Genome Services

Integrated epigenomics and bioinformatics analysis

Integrated Epigenomics & Bioinformatics

Integrate complementary molecular layers with epigenomic data analysis and custom bioinformatics to generate interpretable biological evidence.

Methylation + Transcriptomics · Chromatin + Expression · Multi‑Layer Integration · Custom Bioinformatics

Explore Integrated Analysis

Featured Epigenomics Sequencing & Profiling Services

Selected Services with Distinct Technical Advantages

Focused capabilities for methylation, chromatin, RNA modification, and transcription factor research.

Whole Genome Bisulfite Sequencing (WGBS)

Achieve whole-genome, single-base resolution 5mC profiling with >99% bisulfite conversion efficiency, well suited for comprehensive methylome discovery and DMR analysis.

→

Human DNA Methylation 935K Microarray

Profile 935,000+ CpG sites with a standardized array workflow for cohort, disease, tumor epigenetics, and FFPE studies.

→

Hi-C Sequencing

Study A/B compartments, TADs, and chromatin loops for 3D genome and long-range regulatory research.

→

ChIP-seq

A well-established approach for genome-wide profiling of transcription factor binding and histone marks, ideal for identifying regulatory elements and investigating gene regulation, chromatin states, and disease-associated epigenetic changes.

→

MeRIP-seq

Generate transcriptome-wide m6A enrichment profiles for broad RNA modification screening and multi-condition comparison.

→

DAP-seq

Map transcription factor binding without a TF-specific antibody, ideal for plants, crops, and non-model organisms.

→

Featured Epigenomics Solutions

From Epigenomic Profiles to Focused Research Decisions

CD Genomics provides integrated epigenomics solutions for a broad range of research applications, from biological aging and biomarker discovery to disease mechanisms and therapeutic target research. Our support spans study design, epigenomic profiling, sequencing, bioinformatics, and customized analysis strategies tailored to each research question.

Epigenetic clock and biological aging research

Epigenetic Clock Analysis

Estimate biological age and age-acceleration metrics from DNA methylation data using established or customized epigenetic clock models.

DNA Methylation · Biological Age · Clock Model Selection

Explore Epigenetic Clock Analysis

Cancer Epigenetic Biomarker Discovery

Identify and prioritize candidate biomarkers by integrating DNA methylation, hydroxymethylation, chromatin, and regulatory evidence.

DNA Methylation · 5hmC · Chromatin · cfDNA · Biomarker Prioritization

Explore Cancer Biomarker Discovery

Drug Target Discovery with Epigenomics

Integrate epigenomic and expression evidence to identify disease-associated regulatory mechanisms and prioritize potential therapeutic targets.

Epigenomic Profiling · Multi-Omics Integration · Target Prioritization

Explore Drug Target Discovery

Technology Platforms for Epigenomics Research

Core Platforms Matched to the Study Design

Our workflows combine sequencing, microarray, and mass spectrometry platforms to support diverse epigenomic research needs.

Next-Generation Sequencing

High-throughput sequencing for DNA methylation, chromatin profiling, RNA modification, and 3D genome studies.

Illumina NovaSeq 6000 · NovaSeq X

Long-Read Sequencing

Investigate native DNA and RNA modifications, long-range molecular features, and complex genomic regions.

Oxford Nanopore PromethION · PacBio Revio

Microarray & Targeted Profiling

Support standardized methylation profiling and targeted enrichment for focused studies and large research cohorts.

Illumina iScan · Agilent SureSelect

LC–MS/MS

Quantitative mass spectrometry workflows for DNA, RNA, histone, and protein modification analysis.

Agilent Triple Quadrupole LC/MS · Thermo Scientific Orbitrap

How We Support Your Epigenomics Project

From Study Design to Epigenetic Analysis and Interpretation

CD Genomics supports epigenomics projects from study design and method selection through experimental analysis, quality control, bioinformatics, and data delivery. Our broad capabilities allow project strategies to be shaped around the biological question, study design, and analytical objectives.

Broad Epigenomics Portfolio

DNA methylation · RNA modification · Chromatin · 3D genome · Molecular interactions

Flexible Sample Support

Tissue · Cells · Blood · Plasma & cfDNA · FFPE · Genomic DNA · RNA

Complementary Technology Platforms

NGS · Long-read sequencing · Microarray · Targeted profiling · LC–MS/MS

Integrated Bioinformatics

Single-assay analysis · Multi-layer integration · Custom analytical strategies

Epigenomics project planning and experimental workflow

Project Strategy Research Question + Study Design + Project Constraints → Fit-for-Purpose Epigenomics Strategy

Study Design & Assay Fit

We evaluate suitable approaches before project launch based on resolution, genomic coverage, input requirements, cohort size, and the biological comparison. The goal is to select an assay that fits the question, not simply the most comprehensive method.

Controls, Replicates & Batch Planning

Experimental design is reviewed before samples enter the workflow, with attention to biological replicates, assay-appropriate controls, comparison groups, and batch structure to reduce avoidable confounding.

Pre-Run Feasibility Review

Sample condition, assay compatibility, required output, and downstream analysis needs are reviewed before experimental work begins. Potential limitations can be identified early, before significant project resources are committed.

Assay-Specific QC at Critical Checkpoints

QC is adapted to the selected assay rather than applied as a generic sequencing checklist. Relevant checkpoints may include library performance, sequencing quality, mapping, enrichment or conversion performance, and signal quality.

Analysis Built Around the Study Comparison

The analytical plan follows the biological comparison defined during study design. Contrasts, genomic regions, differential signals, and candidate features are organized around the research question rather than a generic collection of plots.

Interpretable Deliverables & Follow-Up Planning

Results are organized into processed data, key figures, tables, and project reports linked to the original study objective. Important findings, limitations, and candidates for targeted validation or follow-up experiments can be clearly identified.

Scientific Evidence & Featured Client Research

Peer-Reviewed Research Supported by Our Epigenomics Services

Selected peer-reviewed studies highlight how our epigenomics services have supported diverse research questions across DNA methylation, chromatin regulation, RNA modification, aging, cancer biology, and related areas.

Cell Stem Cell · 2024

Cross-Species Trophoblast Epigenomics

Whole-genome DNA methylation profiling supported comparative investigation of trophoblast biology in human and marmoset stem cell models.

WGBS · DNA Methylation · Comparative Epigenomics

View Study

Pancreatic cancer chromatin regulation research

Nature Communications · 2023

Chromatin Regulation in Pancreatic Cancer Stem Cells

ChIP-seq · RNA-seq · Integrated Regulation

View Study

American Journal of Physiology · 2025

m6A Regulation in Liver Regeneration

MeRIP-seq · RNA Modification

View Study

Hypothalamus DNA methylation and aging research

Nature Communications · 2024

Age-Related DNA Methylation in the Hypothalamus

Targeted Bisulfite Sequencing · DNA Methylation · Aging Research

View Study

Latest in Epigenomics

New Technologies, Practical Resources, and Updates

Stay current with newly available methods, project-planning resources, and activity from CD Genomics Epigenetics.

New Technology

m6A-Atlas Antibody-Free m6A Sequencing

Map high-confidence candidate m6A sites across the transcriptome at single-nucleotide resolution without antibody enrichment. Qualified projects can start from as little as 10 ng total RNA, making m6A-Atlas well suited to precious or limited samples and studies requiring precise site-level information.

Explore m6A-Atlas

Resource

What Can WGBS, RNA-Seq, ATAC-Seq, and ChIP-Seq Reveal Together?

See how DNA methylation, chromatin accessibility, protein–DNA binding, and gene expression can be combined into a stronger evidence chain for mechanism-focused epigenomics research.

Read Article

News & Updates

Connecting with Epigenetics Researchers at the 2026 International Symposium on Epigenetic Inheritance

CD Genomics joined researchers from the international epigenetics community in Baton Rouge to exchange ideas on RNA modification, epigenetic inheritance, DNA methylation, and emerging sequencing technologies.

Researchers from numerous laboratories engaged with our team about ongoing and planned studies. Several discussed project-specific sample and study-design challenges and expressed interest in working with CD Genomics on future epigenomics projects.

CD Genomics at Epigenetic Inheritance Symposium 2026

Start Your Epigenomics Project

Ready to Start Your Project?

Tell us about your research needs. Our team can help evaluate suitable approaches and support your project from study design to data delivery.

Helpful details to include (optional)

Sample type & number · Organism & study groups · Research goal or service · Analysis needs or timeline

Sample Guidelines Bioinformatics & Data Analysis