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Methylation Data Analysis

Methylation Data Analysis Online Inquiry

DNA methylation is a functional modification that does not alter gene sequence and is usually located in CpG dinucleotides. Methylation modifications are also present in various transcripts. Methylation is involved in altering and maintaining chromatin state and regulating gene transcription. CD Genomics provides comprehensive DNA/RNA methylation data analysis services and multi-omics data analysis solutions based on data characterization generated by various sequencing technologies and microarrays.

DNA and RNA Methylation

Methylation in DNA and RNA is involved in various processes in human cells, including transcriptional regulation, X chromosome inactivation, genomic imprinting, transposon inactivation, embryonic development and chromatin structural modifications. DNA/RNA methylation is not only involved in gene regulation, but is also associated with the development of various diseases (e.g., cancer) and aging, and methylation patterns in various tissues are also associated with ongoing environmental exposures. Therefore, methylation analysis is an important element in disease mechanism studies and epigenomic research.

DNA methylation, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), etc., is the most clearly studied epigenetic modification. Regions with high CpG density are defined as CpG islands (CGIs). CpG sites occur in a non-random distribution throughout the genome in CpG islands and surrounding regions. m6A is the most common methylation modification present in various transcripts and RNA classes. Nucleic acid methylation can be measured directly at the target site by arrays or more extensively by restriction enzyme and affinity enrichment-based sequencing methods.

What Do We Analyze?

Detection of CpG-rich regions in the entire genome at base-resolution

Complete genomic coverage of methylation at each CpG and less common non-CpG sites (e.g., CNG)

Immunoprecipitation and enrichment of methylated DNA using specific methylcytosine antibodies, followed by high-throughput sequencing to identify the majority of CpG and analyze DNA methylation/hydroxymethylation

Combining next-generation sequencing with m6A RNA immunoprecipitation

Interrogation of the methylation status of thousands of CpG sites with pre-designed probes, including the cancer methylationome, providing sensitivity and specificity

Analysis of DNA methylation data at the single cell level helping reveal the role of this epigenetic marker in processes such as cell division, development and disease progression

Our Data Services Includes

Methylation Data Analysis

  • Raw sequencing data process and quality control
  • Calculation of methylation levels
  • Differentially methylated CpG (DMC) and differentially methylated region (DMR) analysis to decipher disease mechanisms
  • Comparison of relative abundance of enriched fragments
  • Differential binding analysis

How We Can Help You

  • Methylation analysis (methylation microarrays and sequencing) 
  • Meta-analysis of different samples using methylation data generated from multiple studies
  • Combining open and custom genomic data available for downstream analyses such as EWAS
  • Integration of genomic and epigenomic information for association analysis between copy number variation (CNV) and methylation changes
  • Integrating other omics data for further analysis, including RNA-Seq, ChIP-Seq, ATAC-seq, etc., to reveal the relationship and characteristics between methylation and chromatin states
  • If you do not have data generated, please contact us for project design and sequencing services

How It Works

How It Works

Why Choose Us

  • Experienced team to manage all data, determine the most appropriate statistical methods and provide biological interpretation of the results
  • Interactive data analysis reports, including all analysis methods and results
  • Technical support from our lead analyst upon receipt of our data analysis reports
  • High-capacity computing and secure data storage
  • Customized deliverable including FastQC, differential methylation analysis, methylation annotation, and pathway analysis

Explore Applications

Cancer Research

In many types of cancer, DNA methylation leads to widespread gene silencing. An overall decrease in methylation levels in the CpG region can lead to genomic instability. Methylation studies are increasingly used in tumor biomarker screening, tumor detection and monitoring research.

Toxicology Research

Epigenetic reprogramming is susceptible to induction and alteration by environmental factors, such as drug abuse, UV and high-fat diets. Exogenous environmental stresses may alter DNA methylation patterns affecting health and behavior.

Aging Research

Epigenetic alterations are one of the hallmarks of aging. DNA hypomethylation is directly proportional to the rate of cellular senescence. Therefore, DNA methylation is a mechanism for programmed accumulation of mutations with aging as well as a marker for detecting senescence.

Plant Epigenetics

Plants are important for studying epigenetic regulation, and researchers have mapped DNA methylation modifications in models such as Arabidopsis thaliana to reveal epigenetic mechanisms of plant growth, yield, and stress resistance.

* For Research Use Only. Not for use in diagnostic procedures.
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