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メチル化データ解析

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ゲノムメチル化研究に利用できる数ある選択肢から、ゲノムカバレッジの幅に基づき、実施可能なプロジェクトは以下の通りです。

  • Whole Genome Bisulfite Sequencing/全ゲノムバイサルファイトシーケンシング(WGBS)全ゲノムをカバーします。
  • Reduced Representation Bisulfite Sequencing /(RRBS)プロモーターのCpGが豊かな領域に限定されています。
  • Bisulfite Amplicon Sequencing バイサルファイトアンプリコンシーケンス(BSAS)対象領域に限定(少数の遺伝子)

シトシンの解像度に基づき、解析可能な箇所は以下の通りです。

  • 単一塩基スケール(CpGコンテキストの各シトシン– WGBS、RRBS、BSAS、EPICなど)
  • Enrichment based method 濃縮ベース方法(MeDIP-Seq)

解析と一緒に提供されるもの

  • 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.

イベント

  • ChIP workshop
    Diagenode
    Sep 21-Sep 22, 2021
  • DNA methylation workshop: Master MeDIP assay
    Diagenode
    Sep 30, 2021
  • DNA methylation workshop: Become an expert at RRBS
    Diagenode
    Oct 1-Oct 31, 2021
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