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Targeted DNA methylation service

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Catalog Number
Format
G02070000

Targeted DNA methylation analysis allows for the quantitative study of cytosine methylation at known and precise locations throughout the genome. Depending on the size of the region of interest, a number of methodologies can be employed including bisulfite pyrosequencing, bisulfite amplicon sequencing (BSAS), and custom capturing with probes. These techniques share a common methodology of bisulfite conversion followed by sequencing in order to quantitatively detect the methylation status of the target regions at single nucleotide resolution.

  • Description

    Targeted DNA methylation service

    Description

    Best adapted applications

    Bisulfite Pyrosequencing
    • Bisulfite-converted DNA regions  PCR-amplified.
    • One PCR strand sequenced on PyroMark
    • Assay design, primers, and PCR conditions validated
    • Species: human, mouse, rat, and monkey

    Small number of single CpGs or short DNA regions with most of the researcher’s CpGs of interest

    Bisulfite Amplicon Sequencing (BSAS)
    • Bisulfite-converted DNA and target region(s) amplified with several PCR amplicons.
    • Amplicons sequenced using Illumina® platform.
    • Assay, primer design, PCR conditions optimized
    • Species: human

    Several, long DNA regions -- total size up to 200kb

    Custom capture probes
    • Target region(s) selectively captured with  custom-designed RNA baits (Agilent SureSelect).
    • Captured regions are bisulfite-converted and sequenced on Illumina® platform.
    • Species: human

    Large number of very long DNA regions -- total size between 0.2-24Mb
  • Bioinformatic analysis

    Bisulfite Pyrosequencing

    Output files:

    • PCR primers and PCR condition
    • PDF file with raw pyrograms  
    • Excel file with methylation percentage of each target CpG

    Bisulfite Amplicon Sequencing (BSAS)

    Output files:

    • Report with sequencing and CpG methylation statistics
    • FASTQ files with the original raw reads
    • FastQC and trimming reports for the quality of the sequenced reads  
    • Alignment files in BAM format  
    • Alignment and methylation reports  
    • Methylation files of covered Cytosine in bedGraph

    Custom capture probes

    Output files:  

    • Report with sequencing and CpG methylation statistics
    • FASTQ files with the original raw reads
    • FastQC and trimming reports for the quality of the sequenced reads  
    • Alignment files in BAM format
    • Alignment and methylation reports  
    • Methylation files of covered Cytosine in bedGraph

    Differential methylation analysis for any service is available upon request.

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