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:
- Alignment of MeDIP-Seq reads to reference genome;
- Distribution for uniquely mapped reads;
- Genome coverage varies with sequencing depth
- Coverage of CpG sites varies with sequencing depth
- 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)
- Reads distribution for different GC%
- Enriched regions – Peaks
- Statistics for peaks (peak count, average length, median length, genome coverage)
- Genes related to peaks
- Peak distribution in different gene features (as detailed above).
- Differentially methylated genes
- Differentially methylated genes detection based on peaks
- GO enrichment analysis and KEGG pathway analysis for differentially genes
Personalized analysis:
- Estimation of methylation levels (known methylation rate required) in the whole genome and the peaks
- Estimation of methylation levels (known methylation rate required) in differentially methylated regions (DMRs).
- DMR detection
- DMR-associated gene identification
- GO enrichment analysis and KEGG pathway analysis for DMR-associated genes
- Additional personalized analysis needs can be provided.