DNA Methylation profiling
Introduction
DNA methylation is the most studies epigenetic modification that plays an important role in regulating gene expression. The advances in microarray and sequencing technologies make genome‐wide profiling possible at a single‐nucleotide resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis. Due to the increasing need to compute high‐throughput epigenomic data, Molsys Scientific offers services in interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). We provide support in different experimental approaches for profiling genome-wide methylation profiling as follows:
•Whole‐genome bisulfite sequencing (WGBS)
•Methylation array based profiling using Illumina’s Infinium Human Methylation 450 BeadChip (HM450K) protocol
Applications
•Global view of gene activity
•Novel gene and splice variant discovery
•Chromosomal rearrangement analysis
•Whole mRNA transcript expression analysis
Data Analysis
Primary Analysis
•Global methylation profiles
•Specific methylation profiles
- CpG Islands
- Differentially Methylation Regions (DMRs)
Secondary Analysis
•DMRs associated genes
•Gene set enrichment analysis
•Comparative Analysis
Sample Type
Genomic DNA
Required amount ≥ 2.5 μg;
Purity - OD 260/280 = 1.8 - 2.0
Platform Type
Illumina Novaseq 6000
Read Length
Paired-end 150
Recommended Sequencing Depth ≥ 30× coverage for the species with reference genome
Standard Data Analysis
•Data quality control
•mCs detection, methylation level calculation
•Methylation level and frequency distribution
•Differentially Methylated Site (DMS) detection
•Differentially methylated regions (DMRs), Differentially Methylated Promoter (DMPs) detection and annotation
•Function enrichment of DMR-associated genes and DMP-associated genes
•Visualization of BS seq data
•Comparative analysis (among samples)
