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MeDIP Sequencing (MeDIP-Seq)

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MeDIP Sequencing (MeDIP-Seq)

CD Genomics is providing Methylated DNA Immunoprecipitation Sequencing (MeDIP) service to enrich and capture methylated DNA fragments for use in gene-specific DNA methylation studies on a genome wide scale.

DNA modifications, such as methylation and hydroxymethylation, are pivotal players in modulating gene expression, genomic imprinting, X-chromosome inactivation, and silencing repetitive sequences during embryonic development. In mammals, methylation occurs at cytosine bases which are followed by a guanine base (CpG), principally in the form of 5-methylcytosine. Comprehensive genome-wide DNA methylation and hydroxymethylation studies provide a way to thoroughly understand normal development and to identify potential epigenetic mutations.

MeDIP-seq is the method combining methylated DNA immunoprecipitation combined with next-generation sequencing. It uses an anti-5-methylcytosine antibody coupled to magnetic beads to select for genomic fragments that are methylated. These fragments are then sequenced and the coverage of these reads can be used to estimate the methylation level of the region that they map to. The sixth DNA modification 5-hydroxymethylcytosine (5hmC) can also be detected genome-wide by using a hydroxymethylated DNA immunoprecipitation (hMeDIP) procedure with a 5hmC-specific antibody. MeDIP-seq neither introduces any mutations nor requires uracil-tolerant DNA polymerase. MeDIP-seq technology is feasible to profile genome-wide DNA methylation in low amounts of DNA samples with the resolution of several hundred base pairs in minimal selection bias and at a competitive cost. The workflow of a typical MeDIP-seq is demonstrated in the below Figure 1. Briefly, the extracted DNA is fragmented, denatured, ligated with adaptor and captured using the antibody directed against 5 methylcytosine and antibody binding beads, the enriched methylated DNA is then amplified with PCR. The samples are size-selected and sequenced on Illumina sequencing instrument.

 Figure  1.  Schematic workflow of MeDIP  sequencing process. Figure 1.  Schematic workflow of MeDIP sequencing process.

Sequencing Strategy and Recommended Sequencing Depth

  • Illumina HiSeq 2500 PE100
  • 50 M reads or 4-5 Gb data per sample

Data Analysis

We are equipped a team with the expert knowledge and computational resources to help you achieve your data analysis objectives. Our comprehensive bioinformatics solutions for MeDIP sequencing data include alignment with reference genome, sequencing depth and coverage analysis, whole genome region distribution, peak distribution statistics, peak associated gene screening and functional annotation, differential expression level analysis of peak associated genes, and GO/KEGG analysis.

Sample Requirements

  1. Sample Type: Genomic DNA without RNA contamination and severe degradation
  2. Amount: DNA ≥ 5 µg; concentration ≥ 50 ng/µl
  3. Purity: OD260/280 = 1.8~2.0

Key Features and Advantages

  • Fast, high specific, and efficient enrichment of 5-mC containing DNA
  • Low amount of input DNA is required
  • Minimal selection bias and low error rates
  • Comprehensive bioinformatics analysis
  • More affordable than Bisulfite Sequencing by improving the utilization rate of the data

By using reliable methylation capture antibody, high-throughput sequencing technology and professional bioinformatics capability, CD Genomics offers high-quality MeDIP-Seq as an end-to-end, genome-wide epigenetic service to identify differentially methylated regions, and ultimately help to expedite research in these areas.

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