MagMeDIP-seq Package V2
MeDIP-seq library prep. kit for low DNA amount

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Catalog Number
10 rxns

Perform MeDIP-seq experiments, i.e. methylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.

MeDIP-seq methods allow you to:

  •     Perform genome-wide DNA methylation mapping
  •     Detect and identify differentially methylated regions with high sensitivity
  •     Get better insight of your epigenetics research

Diagenode's MagMeDIP-seq package V2 has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the lowest DNA amounts  and secure high-quality NGS data for DNA methylation analysis. Only 10 ng of sheared genomic DNA is required for IP enrichment and library generation, while preserving the efficiency of the enrichment.

The package contains everything you need for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.



  • All-in one MeDIP-seq kit, fully validated for NGS analysis
  • Low DNA requirement: down to 10 ng per reaction
  • Robust method, superior enrichment, and easy-to-use protocol
  • High reproducibility between replicates and repetitive experiments

Sequencing analysis

Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores.
MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.

A. Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.

B. Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.

  • Validation: Sequencing quality

    Figure 2. Excellent sequencing quality. Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).

    Figure 3. Saturation analysis. Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible between replicates and repetitive experiments (data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).

  • Validation: Peak search

    Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.

    Figure 5. Annotation of significant methylated regions detected on human blood samples. The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).

  • Validation: Control regions

    Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).

    Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).

  •  Documents
    MagMeDIP-seq package v2 MANUAL
    Magnetic Methylated DNA Immunoprecipitation Package for Illumina sequencing
    DNA Methylation Solutions BROCHURE
    Complete solution for DNA methylation studies! Whether you are experienced or new to th...
  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: MagMeDIP-seq Package V2
    MeDIP-seq library prep. kit for low DNA amount (Diagenode Cat# C02010041)
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    Using our products in your publication? Let us know!

    Polycystic ovary syndrome is transmitted via a transgenerational epigenetic process
    Mimouni et. al.
    Polycystic ovary syndrome (PCOS) is the most common reproductive and metabolic disorder affecting women of reproductive age. PCOS has a strong heritable component, but its pathogenesis has been unclear. Here, we performed RNA sequencing and genome-wide DNA methylation profiling of ...

    Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer.
    Cao F, Wei A, Hu X, He Y, Zhang J, Xia L, Tu K, Yuan J, Guo Z, Liu H, Xie D, Li A
    BACKGROUND: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the det...

    Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes.
    Nassiri F, Chakravarthy A, Feng S, Shen SY, Nejad R, Zuccato JA, Voisin MR, Patil V, Horbinski C, Aldape K, Zadeh G, De Carvalho DD
    Definitive diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Noninvasive diagnostic approaches provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. In the present study, we show that DNA-methylation profiles from plasma reveal highly specific sign...

    Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes.
    Nuzzo PV, Berchuck JE, Korthauer K, Spisak S, Nassar AH, Abou Alaiwi S, Chakravarthy A, Shen SY, Bakouny Z, Boccardo F, Steinharter J, Bouchard G, Curran CR, Pan W, Baca SC, Seo JH, Lee GM, Michaelson MD, Chang SL, Waikar SS, Sonpavde G, Irizarry RA, Pome
    Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all ...

    Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA.
    Shen SY, Burgener JM, Bratman SV, De Carvalho DD
    Circulating cell-free DNA (cfDNA) comprises small DNA fragments derived from normal and tumor tissue that are released into the bloodstream. Recently, methylation profiling of cfDNA as a liquid biopsy tool has been gaining prominence due to the presence of tissue-specific markers in cfDNA. We have previously reporte...

    DNA methylation of the Tacr2 gene in a CUMS model of depression.
    Xiang D, Xiao J, Fu L, Yao L, Wan Q, Xiao L, Zhu F, Wang G, Liu Z
    Tacr2, the gene encoding the NK2 receptor, belongs to G protein-coupled receptors. Accumulating evidence has indicated that the tachykinin receptors may contribute to the pathophysiology of depression. During the last decade, some studies have shown that Tacr2 activation is involved in the modulation of emotional pr...

    Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
    Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPher
    The use of liquid biopsies for cancer detection and management is rapidly gaining prominence. Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these methods may be low among patients with early-stage cancer given the limited ...

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