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CD Genomics is providing a novel, flexible, and scalable genome-wide DNA methylation profiling method, MethylRAD, to allow for de novo methylation analysis with extremely low DNA input.

The Introduction of MethylRAD-Seq

MethylRAD uses methylated modified dependent endonuclease, such as FspEI, MspJI, LpnPI, AspBHI, etc., to recognize cytosine methylated on DNA and cut double chains at a distance downstream of the recognition site, and if the DNA double-strand has a central symmetric methylation state, a fixed length of double-strand DNA fragment can be cut and then sequenced. DNA methylation is a heritable epigenetic mark and plays a vital role in many biological processes such as embryogenesis, cellular differentiation, X-chromosome inactivation, genomic imprinting and transposon silencing, perturbed methylation patterns are sometimes a hallmark of important human diseases. Profiling the DNA methylation landscape and its dynamics enable researchers to look deeply into key epigenetic mechanisms that modulate development and diseases. MethylRAD allows for de novo (reference-free) methylation analysis, extremely low DNA input (e.g. 200 ng) and adjustment of tag density, all of which are still unattainable for most widely used methylation profiling methods such as RRBS and MeDIP sequencing.

Key Features and Advantages of MethylRAD-Seq

  • Extremely low amount of input DNA required
  • Adjustable tags density
  • High specificity, sensitivity and reproducibility
  • Allows for de novo methylation analysis
  • Ideally suited for large-scale methylation profiling
  • Comprehensive bioinformatics analysis
  • Suitable for most species especially plant species

MethylRAD-Seq Workflow

The MethylRAD-Seq Workflow is outlined as below:

Service Specification

Sample requirements and preparation

  • DNA amount ≥ 200 ng; DNA concentration ≥ 25 ng/μl, OD260/280=1.8~2.0
  • Sample Type: Genomic DNA without RNA contamination and severe degradation

Bioinformatics Analysis

  • Removal of adapters and low-quality reads, statistics of sequencing depth and coverage
  • Assembly and mapping the reads to reference genome
  • Genome-wide distribution of methylation sites, annotation and statistics
  • Distribution of methylation site on the function elements
  • Density of methylation sites
  • Relative quantification of DNA methylation levels
  • DNA methylation pattern profiling
  • Comparisons of methylation levels between different groups and analysis of methylation differential genes
  • More data mining upon your request

Analysis pipeline


  • The original sequencing data
  • Experimental results
  • Data analysis report
  • Details in MethylRAD for your writing (customization)

CD Genomics uses a simple and flexible method for genome-wide DNA methylation profiling with high specificity, sensitivity and reproducibility, enabling de novo methylation analysis with extremely low DNA input, and flexible adjustment of tag density. If you have any questions, please feel free to contact us.

* For Research Use Only. Not for use in diagnostic procedures.
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CD Genomics
CD Genomics-the genomics service company