Whole Bisulfite Analysis

Methylation of DNA at C5 position of cytosine impacts various cellular processes involving gene expression and chromatin remodeling. These plays a vital role in processes associated with health and development through methylation of promoter regions, cell differentiation, remodeling of chromatin, transposon silencing, etc. Eurofins genomics offers comprehensive whole genome bisulfite analysis which is an effective method to analyze methylation of whole genomes. Eurofins has built up a proprietary pipeline to provide cost-efficient methods to customer.

Workflow & Deliverables

Bioinformatics workflow for Whole Genome Bisulfite analysis:

a. Quality check of raw reads

The raw reads will be subjected to quality filtration and adapter trimming. The high quality data will be used for downstream analysis.

b. Alignment of whole genome bisulfite sequencing reads against reference genome

High quality reads will be aligned to the reference genome. Bismark will be used for the bisulfite converted genome alignment. Bismark is a set of tools, specifically used for the analysis of bisulfite-sequence (BS-Seq) reads. It uses Bowtie and Bowtie2 for aligning the reads.

c. Methylation Profiling

Basically, it produces methylation calls based on three different contexts:

1) CpG context

2) CHG context (where H is A, C or T)

3) CHH context.

d. Detection of Differentially Methylated Sites (DMS), Differentially Methylated Regions (DMRs) and Differentially Methylated Promoter (DMPs) and their annotations

e. Functional enrichment analysis of genes associated with DMRs and DMPs

Deliverables

• Quality filtration of data,
• Genome alignment to the insilico converted bisulphite genome,
• Alignment files in .bam format,
• Methylation density/Genome wide methylation profile identification,
• Differentially methylated Genes,
• Gene ontology of shortlisted genes (if available)
• Shortlisted genes Pathway analysis (if available)
• Compiled report