Q1. Can you assist with primer design for my loci of interest?

Yes. We can review any primers you've already designed or create new ones tailored to your targets—optimized for CpG richness, GC content, melting temperature, and amplicon size to ensure specificity and efficiency.

Q2. How many genomic sites can I include per assay run?

The service is flexible. Whether you're validating a single locus or a panel of multiple genes, we'll adapt our workflow and cost structure to suit your list of targets.

Q3. What quality controls are built into the assay?

Each assay includes Input DNA for normalization and an IgG control to monitor specificity. If you prefer, we can also include positive reference loci or synthetic spike-in controls for benchmarking.

Q4. Are 5mC and 5hmC assays compatible with each other?

Yes—they are entirely compatible. Distinct antibodies are used in each assay, so you can run them separately or in parallel to compare methylation versus hydroxymethylation dynamics at the same region.

Q5. What if I have limited or degraded DNA?

No worries—just let us know your sample constraints upfront. We can run a pre-check on DNA integrity, suggest adjustments like altered fragmentation settings, and propose strategies to maximize success from your available material.

Q6. Is this assay meant to follow or support high-throughput data?

Absolutely. If you have preliminary hits from WGBS, MeDIP-seq, or array profiling, this assay provides quantitative locus-specific confirmation—perfect for validating your discoveries with confidence.

Q7. What deliverables will I receive once the assay is complete?

You'll get the raw Ct files, normalized enrichment tables, clear visual graphs, and a concise Methods summary—packaged for transparency, reproducibility, and ease of use in your manuscripts.

MeDIP-qPCR & hMeDIP-qPCR Services – Locus-Specific DNA Modification Validation

High-throughput assays uncover genome-wide candidates, but researchers often need locus-specific confirmation. MeDIP-qPCR and hMeDIP-qPCR deliver quantitative insight into 5mC and 5hmC at defined genomic regions, adding clarity and confidence to your epigenetic research.
Key Highlights

Locus-specific quantification of 5mC and 5hmC
Reliable follow-up to sequencing or array findings
High sensitivity and reproducibility with built-in controls
Publication-ready data presentation

Get a Quote

MeDIP-qPCR & hMeDIP-qPCR showing DNA fragmentation, antibody enrichment, and qPCR readout.

Introduction

From Genome-Wide Discovery to Locus-Specific Confidence

High-throughput assays such as WGBS, MeDIP-seq, or array profiling provide a powerful genome-wide overview of DNA methylation and hydroxymethylation. They are essential for identifying candidate regions and building the big picture. Yet when the focus shifts to a single promoter, CpG island, or regulatory element, researchers need confirmation that goes beyond statistical predictions.
This is where MeDIP-qPCR and hMeDIP-qPCR play a complementary role. By combining antibody-based enrichment with quantitative PCR, they deliver:

Direct experimental confirmation – moving from computational signals to validated results.
Quantitative resolution – ΔCt-based enrichment values that provide measurable confidence.
Complementary strength – not a replacement for high-throughput assays, but the natural next step to refine and validate discoveries.

Together, genome-wide discovery and locus-specific validation form a complete workflow: broad exploration identifies where to look, while MeDIP-qPCR and hMeDIP-qPCR provide the clarity to confirm what truly matters.

Advantages

Nuanced Touches That Strengthen Your Results

Not all enrichment-qPCR assays are equal. Subtle technical decisions can make the difference between ambiguous data and interpretable results. Our service pays attention to these critical details:

Primer design support – either reviewing your sequences or designing new primers optimized for CpG density, GC content, and amplicon size.
Comprehensive control strategy – including Input DNA for normalization, IgG negative controls, and positive reference regions to benchmark enrichment.
Optimized enrichment conditions – controlled DNA fragmentation (400–500 bp) and validated antibodies specific for 5mC or 5hmC.
Flexible scope – from single-locus validation to multi-gene panels, with workflows adapted to your research goals.

These technical refinements ensure that enrichment values are meaningful, reproducible, and ready to inform your next research step.

Your Professional Advantage

Choosing the right partner for locus-specific epigenetic validation can make a critical difference in the reliability of your findings. Our MeDIP-qPCR and hMeDIP-qPCR services are designed with researchers in mind:

Scientist-driven design – every project is overseen by experts familiar with the nuances of DNA modification analysis, from antibody specificity to primer optimization.
Rigorous quality control – input normalization, negative controls, and validated enrichment conditions ensure reproducible and interpretable results.
Publication-ready outputs – data packages include raw files, processed enrichment values, figures, and concise documentation suitable for Methods sections.
Integration with your workflow – whether you are validating high-throughput discoveries or focusing on hypothesis-driven loci, our assays slot seamlessly into existing projects.
Confidentiality and reliability – secure handling of samples and data, with transparent processes you can trust.

By combining technical precision with researcher-focused support, we provide not just an assay, but a dependable extension of your lab capabilities.

Service Workflow

Service Workflow – From DNA to qPCR Readouts

Our workflow is designed to deliver locus-specific clarity while maintaining reproducibility at every step:

1. DNA Quality Control & Fragmentation

Genomic DNA is assessed for integrity, then sheared into 400–500 bp fragments suitable for immunoprecipitation.

2. Denaturation & Sample Splitting

DNA is denatured into single strands and divided into two groups: one for enrichment (IP) and one as the Input control.

3. Antibody Enrichment

Target-specific antibodies capture either 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC).
Non-modified DNA fragments are washed away, leaving enriched DNA bound to antibody complexes.

4. DNA Purification

The enriched DNA is released and purified, ensuring it is free of inhibitors for downstream amplification.

5. qPCR Detection

Locus-specific primers amplify the regions of interest.
Ct values are obtained for both IP and Input DNA.

6. Relative Enrichment Calculation

Modification levels are quantified using ΔCt normalization, producing fold-enrichment values that reflect true biological differences.

Workflow of MeDIP-qPCR and hMeDIP-qPCR showing DNA shearing, denaturation, antibody selection, immunoprecipitation, DNA isolation, and qPCR.

Each stage integrates quality controls to safeguard data integrity, so the final readout is not only quantitative but also biologically meaningful.

Bioinformatics

Bioinformatics Analysis – Making Data Actionable

The value of MeDIP-qPCR and hMeDIP-qPCR lies not only in generating Ct values but in transforming those numbers into interpretable results. Our bioinformatics analysis pipeline ensures that every dataset is delivered in a format researchers can immediately use:

Step	What We Do	What You Get
Raw Data Processing	Export Ct values from IP and Input samples; perform QC checks	Ct tables and quality summary
Normalization & Enrichment	Apply ΔCt normalization against Input; calculate fold-enrichment	Locus-specific enrichment values (Excel/CSV)
Comparative Analysis	Compare treated vs. control groups or biological replicates	Differential enrichment tables
Visualization	Generate plots (bar charts, box plots, heatmaps)	Publication-ready figures
Integration (Optional)	Align validation results with WGBS, MeDIP-seq, or array data	Combined interpretation linking HTS + qPCR

Deliverables

Deliverables – What You Receive

Following the analysis, you will receive a complete data package designed to be both transparent and ready for direct use:

Raw files – original qPCR output and Ct values

Processed data – normalized enrichment results in Excel/CSV format

Comparison results – enrichment differences across groups or conditions

Figures – clear visual outputs for reports or publications

Methods & QC summary – concise documentation suitable for Materials & Methods

Primer details (if applicable) – sequences and QC notes for primer sets designed by us

Sample Requirements

Sample Requirements & Submission Guidance

Category	Guidance
Accepted Sample Types	Cells, tissue, blood, or purified DNA. Other sample types may be discussed in advance.
Recommended Amounts	- Cells: ~5 × 10⁶ cells - Tissue: >50 mg - Blood: >2 mL whole blood (EDTA tubes recommended; do not use heparin) - DNA: 3–10 µg (≥50 ng/µL, intact, RNA-free)
Storage & Shipping	- Place samples in 1.5 mL tubes, sealed securely, ship on dry ice. - Tissue: rinse with PBS, freeze in cryotubes with liquid nitrogen, then transfer to –80°C. - DNA: dissolve in nuclease-free water, store at –80°C, avoid repeated freeze–thaw cycles.

Applications

Applications – Where These Assays Advance Your Work

MazF-qPCR is designed for researchers who require site-specific, quantitative validation of m6A modifications. Typical use cases include:

Validation of high-throughput findings

Confirm differentially methylated regions identified by WGBS, MeDIP-seq, or array-based profiling with direct qPCR evidence.

Epigenetic dynamics in development and differentiation

Track how 5mC and 5hmC levels evolve across developmental stages, lineage commitment, or induced reprogramming.

Treatment and environmental response models

Detect locus-specific changes following drug exposure, stress conditions, or environmental perturbations.

Mechanistic insights into disease research

Explore how locus-specific methylation or hydroxymethylation shapes transcriptional regulation in disease models.

Comparative interpretation of 5mC vs 5hmC

Disentangle the biological roles of methylation and hydroxymethylation at the same promoter or regulatory region.

Case Study

MeDIP-qPCR Reveals Epigenetic Mechanism in Glioma

Title: TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation

Journal: Cell Death Discovery (2024)

Authors: Hongyu Xu, Shengrong Long, Chengshi Xu, et al.

Methods: MeDIP-qPCR (together with ChIP-qPCR and RNA-seq)

Summary:

This study uncovered a key epigenetic mechanism in glioma progression. The enzyme TDG (thymine DNA glycosylase), found to be overexpressed in glioma, was shown to promote active DNA demethylation at the promoter region of the extracellular matrix protein gene TNC, leading to its upregulation.

MeDIP-qPCR experiments confirmed reduced DNA methylation and increased TNC expression in glioma models. Functional assays demonstrated that silencing TDG suppressed glioma malignancy, while knockdown of TNC inhibited tumorigenic features and reversed TDG-driven effects. These findings highlight the TDG–TNC axis as a novel epigenetic pathway contributing to glioma development.

Example illustration of MeDIP-qPCR results

FAQ

FAQ – Researcher Questions

Bring Clarity to Your Epigenetic Story

When genome-wide approaches point you to candidate regions, the next step is to confirm them with confidence. MeDIP-qPCR and hMeDIP-qPCR offer the precision to turn broad discovery into solid, locus-specific evidence.

If you're ready to validate your findings, share with us:

Your regions of interest (promoters, CpG islands, or regulatory elements)
The type and condition of your samples
Any prior sequencing or profiling data you'd like us to integrate

Our team will provide a tailored plan that outlines assay design, quality controls, and the format of deliverables. From raw files to clear enrichment values, we ensure you have results that can be directly used for interpretation and publication.

→ Get in touch today to discuss your project and start building reliable evidence for your research.