WGBS service (Whole Genome Bisulfite Sequencing)

QC of the genomic DNA

• Measurement of DNA concentration
• Assessment of DNA quality

Library Preparation

WGBS

• gDNA shearing on Bioruptor Pico (not necessary for cfDNA or FFPE)
• Bisulfite conversion
• Library preparation
• QC of the WGBS libraries (DNA concentration, analysis of the profile)

• gDNA shearing on Bioruptor Pico (not necessary for cfDNA or FFPE)
• Library preparation with Enzymatic conversion
• QC of EM-seq libraries (DNA concentration, analysis of the profile)

Deep sequencing

• Samples are sequenced on Illumina platform, paired-end reads of 150bp length (PE150)  
• 400M raw reads on average per samples (when pooling 6 samples/lane)
• Theoretical Coverage >30X for human, mouse and rat samples
• Detection of >50 million CpGs with 6-9X average CpG coverage for human samples 

• FASTQ raw data
• FASTQC quality control insights
• Alignment of bisulfite sequencing data against reference genome
• Methylation calling and extraction
• Summary statistics

• Methylation level analysis
• Differentially methylated CpGs (DMCs) analysis
• Differentially methylated regions (DMRs) analysis
• Annotation of DMCs and DMRs for genomic regions (exons, introns, …) and for CpG island locations (islands, shores, shelves, ...)
• Clustering analysis

Gene ontology terms analysis

• Enrichment analysis on gene associated with DMCs and DMRs
• Get functional insights

Pathway analysis

• Identification of biological pathways in which genes associated with DMCs and DMRs may be over-represented (or under-represented)
• Get mechanistic insights

Data mining

• Biomarker discovery
• Determination of methylation pattern/signature that can be predictive and discriminate between different groups/conditions

Development and epigenetic plasticity of murine Müller glia.
Dvoriantchikova G, Seemungal RJ, Ivanov D
The ability to regenerate the entire retina and restore lost sight after injury is found in some species and relies mostly on the epigenetic plasticity of Müller glia. To understand the role of mammalian Müller glia as a source of progenitors for retinal regeneration, we investigated changes in gene expres...

The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue.
Dvoriantchikova G, Seemungal RJ, Ivanov D
The epigenetic plasticity of amphibian retinal pigment epithelium (RPE) allows them to regenerate the entire retina, a trait known to be absent in mammals. In this study, we investigated the epigenetic plasticity of adult murine RPE to identify possible mechanisms that prevent mammalian RPE from regenerating retinal...