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Methylation Data Analysis

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Catalog Number
Format
G02020107

There are many alternatives available to study genome methylation. Based on the width of genome coverage, we can undertake projects such as:

  • Whole Genome Bisulfite Sequencing (WGBS) which covers the entire genome
  • Reduced Representation Bisulfite Sequencing (RRBS), limited to CpG-rich regions in promoters
  • Bisulfite Amplicon Sequencing (BSAS), limited to targeted regions of interest (few genes)

Based on the cytosine resolution, the analysis can be made at:

  • Single base scale (for each cytosine in a CpG context – WGBS, RRBS, BSAS, EPIC, etc)
  • Enrichment based method (MeDIP-Seq)

What do we provide with the analysis?

  • Single-base resolution Analysis (WGBS, RRBS, BSAS, EPIC)

    This analysis provides information on each single CpG with its methylation percentage.

    Standard Analysis:

    • Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates (WGBS), number of CpGs detected, average coverage at CpG sites, number of CpGs detected with coverage greater than 10x, etc.)
    • Trimmed and filtered reads in fastQ files after sequencing QC
    • BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)
    • BED files from methylation calling and extraction (CpG location, number of methylated cytosines, number of unmethylated cytosines and coverage at the CpG site)

    Advanced Analysis

    • Comparative analysis (also called differential analysis) aimed at finding differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs) between two groups of samples
    • Annotation of DMCs and DMRs for genomic regions (exons, introns, etc) and for CpG island location (islands, shores, shelves, etc)
    • Gene ontology enrichment analysis on genes associated with DMCs and DMRs
    • Pathway enrichment analysis on genes associated with DMCs and DMRs (KEGG or DOSE for human samples)

    Customized Analysis

    If you require a type of analysis that is not in the previous list, please consult with our expert bioinformatics team.

  • Methylated region resolution Analysis (MeDIP-Seq):

    This analysis provides information on each methylated region (peak) with its level of methylation enrichment for that region.

    Standard Analysis

    • Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates, number of peaks, average peak width, reads in peaks, frequency of reads in peaks, etc.)
    • Trimmed and filtered reads in fastQ files after sequencing QC
    • BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)
    • BED files from peak calling (peak location, peak calling score, peak density)
    • Annotation files with location of the peaks within genes

    Advanced Analysis

    • Comparative analysis (also called differential analysis) aimed at finding differentially methylated regions between two groups of samples as well as the regions specifically methylated in each group of samples
    • Annotation of differentially/uniquely methylated regions with genomic context
    • Determination of specific binding motifs within peaks
    • Gene ontology enrichment analysis on genes associated with differentially /uniquely methylated regions
    • Pathway enrichment analysis (KEGG or DOSE for human samples) on genes associated with differentially/uniquely methylated regions

    Customized Analysis

    If you require a type of analysis that is not in the previous list, please consult with our expert bioinformatics team.

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