MeDIP Sequencing

Methylated DNA immunoprecipitation (MeDIP) is a large-scale (chromosome- or genome-wide) technology that is used for analysing methylated DNA sequences. Methylated DNA fragments are isolated using an antibody raised against 5-methylcytosine (5mC), the purified fraction of methylated DNA then undergoes next generation sequencing. MeDIP-seq is sensitive to highly methylated, high CpG densities.

Workflow

Bioinformatics

Data cleaning:

Data processing includes removing adaptors, contamination, and low-quality data from raw reads.

Standard bioinformatics analysis:

  1. Alignment of MeDIP-Seq reads to reference genome;
  2. Distribution for uniquely mapped reads;
  3. Genome coverage varies with sequencing depth
    1. Coverage of CpG sites varies with sequencing depth
    2. Reads distribution in different genomic features (CpG islands, repeat elements, and gene features, including first exon, first intron, internal exons, internal introns, last exon, upstream 2 K, and downstream 2 K)
    3. Reads distribution for different GC%
  4. Enriched regions – Peaks
    1. Statistics for peaks (peak count, average length, median length, genome coverage)
    2. Genes related to peaks
    3. Peak distribution in different gene features (as detailed above).
  5. Differentially methylated genes
    1. Differentially methylated genes detection based on peaks
    2. GO enrichment analysis and KEGG pathway analysis for differentially genes

Personalized analysis:

  1. Estimation of methylation levels (known methylation rate required) in the whole genome and the peaks
  2. Estimation of methylation levels (known methylation rate required) in differentially methylated regions (DMRs).
    1. DMR detection
    2. DMR-associated gene identification
    3. GO enrichment analysis and KEGG pathway analysis for DMR-associated genes
  3. Additional personalized analysis needs can be provided.