WGBS service (Whole Genome Bisulfite Sequencing)

WGBS services include:

QC of the genomic DNA	Measurement of DNA concentration Assessment of the DNA quality
Preparation of WGBS libraries*	gDNA shearing on Bioruptor® Pico Library preparation (end repair, adenylation, methylated adaptor ligation) Size selection Bisulfite conversion Library amplification QC of the WGBS libraries (DNA concentration, analysis of the profile)
Deep sequencing	Samples are sent for sequencing on an Illumina platform Single-read or paired-end 50bp to 150bp read length Coverage to be defined

*Full protocol details can be viewed in the manual from the Premium Whole Genome Bisulfite Sequencing (WGBS) Kit

Standard analysis

Methylation calling:

Alignment of bisulfite sequencing data to reference genome and determination of methylation status of CpG nucleotides.

Additional analysis on request:

Differential methylation analysis:

Comparison of methylation status of CpG nucleotides between sample groups.

Annotation with genomic regions:

Annotation of differentially methylated CpGs or of DMRs with genomic regions such as introns, exons, enhancers (when available), promoters, intergenic regions.

Gene ontology terms analysis:

Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in differentially bound regions may indicate the underlying biological processes involved.

Pathway analysis:

Identify biochemical pathways in which genes associated with differentially methylated regions (or individual differentially methylated CpGs) may be overrepresented.

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Diagenode strongly recommends using this: WGBS service (Whole Genome Bisulfite Sequencing) (Diagenode Cat# G02040000). Click here to copy to clipboard.

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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...