Single-cell DNA Methylation Sequencing

CD Genomics provides single-cell DNA methylation analysis to understand the heterogeneity of genome-wide 5-methylcytosine (5mC) patterns.

The Introduction of Single-cell DNA Methylation Sequencing

DNA methylation is recognized as a principal contributor to the normal development and regulation of gene expression. It is essential for maintenance of cellular identity and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging and carcinogenesis. The current method to research DNA methylation is only by bulk approach, such as whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and MeDIP sequencing. We combine the highly innovative single cell WGBS library preparation and Illumina next-generation sequencing technology to visualize genomic methylation states at single-cell resolution. Single cell whole genome bisulfite sequencing enables the discovery of cellular heterogeneity typically masked by standard, bulk methylation sequencing. We provide a streamlined workflow for making WGBS libraries. Input DNA is randomly fragmented during the initial bisulfite treatment step followed by WGBS library preparation. The procedure can accommodate ultra-low DNA input making it ideal for methylation analysis of precious, limited, and target-enriched samples.

Single-Cell DNA methylation Sequencing Workflow

With post-bisulfite library preparation for WGBS, the workflow can be completed in a few hours. The general workflow for single-cell methylation sequencing is outlined below.

Single-cell DNA Methylation Sequencing

Service Specifications
Sample requirements
  • 96-well plates of live cells suspension are recommended for this procedure.
  • Frozen cells in specifically frozen lysates can also be used as starting material.
  • >100 pg extracted DNA should be free of enzymatic inhibitors and can be suspended in water, TE, or a low salt buffer.
Flexible service options include HiSeq X
Bioinformatics Analysis
  • Alignment against a reference genome
  • Sequence depth and coverage analysis
  • mC calling
  • Methylation level analysis
  • Global trends of methylome
  • Methylation density analysis
  • Differentially Methylated Regions (DMRs) analysis
  • DMR annotation and enrichment analysis (GO/KEGG)
  • Clustering analysis


  • The original sequencing data
  • Experimental results
  • Data analysis report
  • Details in Single-Cell Sequencing for your writing (customization)

CD Genomics's Single-Cell Sequencing conference focuses on the links between cell variation in tissues and organ function and further elucidates the origins of diseases. If you have additional requirements or questions, please feel free to contact us.


Gravina, S et al. Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome. Genome Biology, 2016 17(1):150.

For Research Use Only. Not for use in diagnostic procedures.
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