Diagenode

MeDIP-seq service (Methylated DNA IP Sequencing)

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Catalog Number
Format
G02050000

Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is used to study 5-mC genome-wide. In this assay, specific antibodies against 5-mC are used to capture methylated DNA regions using an immunoprecipitation assay. The enrichment of methylated DNA in the immunoprecipitated fraction is determined by sequencing to assess the methylation state of individual regions. Using the same approach it is possible to study DNA hydroxymethylation by using an antibody specific for 5-hmC (hMeDIP-seq).

Excellent method for qualitative analysis of DNA methylation profiles

    • Resolution of 100-500 bp
    • 5-mC coverage in low density and highly repetitive regions
    • Antibody-based approach independent of sequence with high specificity and minimal bias
    • Dedicated scientist handles your project with high touch communication
    • Comprehensive service – Immunoprecipitation, library preparation, sequencing, and analysis

 

  • Description

    MeDIP and hMeDIP sequencing services include:

    QC of the genomic DNA

    • Measurement of DNA concentration
    • Assessment of  DNA quality

    Preparation of MeDIP-seq/hMeDIP-seq libraries*

    • gDNA shearing on Bioruptor® Pico  
    • Library preparation
    • Immunoprecipitation of methylated or hydroxymethylation DNA using Abs specific to either 5-mC, 5-hmC
    • Library amplification and clean-up  
    • QC of the MeDIP-seq/hMeDIP-seq libraries

    Deep sequencing

    • Samples are sent for sequencing on an Illumina platform  
    • Single-read or paired-end  
    • 50bp to 150bp read length  
    • Greater than or equal to 50M reads per sample
    • Coverage to be defined with customer

    *Full protocol details can be viewed in the MagMeDIP Kit manual

  • Bioinformatic analysis

    Standard analysis

    Methylation calling:

    Quality check, alignment of sequencing data to reference genome, and identification of methylated or hydroxymethylated regions. Provided files include FastQC reports, alignment files in BAM format, and peak files in BED format.

    Additional analysis on request:  

    Differential methylation analysis:

    Identification of differential methylation or hydroxymethylation between samples based on previously identified MeDIPseq/hMeDIP-seq peaks.  

    Annotation with genomic regions:

    Annotation of MeDIP-seq/hMeDIP-Seq peaks with genomic regions such as introns, exons, enhancers (when available), promoters, intergenic regions.  

    Gene ontology terms analysis:

    Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in differentially bound regions may indicate the underlying biological processes involved.  

    Pathway analysis:

    Identify biochemical pathways in which genes associated with differentially methylated regions (or individual differentially methylated CpGs) may be overrepresented.  


    Visualization of specific genomic regions:

    Visualization of results (i.e. sequencing data, peaks) at specific genomic regions (e.g. genes, promoters) in publication-ready images (human, mouse, rat).

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