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The single-cell whole-genome bisulfite sequencing service from Creative Biolabs can analyze single-cell DNA methylation in a variety of biological systems to explain intercellular epigenetic variability in complicated tissue samples.

Single Cell Whole Genome Bisulfite Sequencing

In mammals, DNA methylation, which occurs mostly at CpG dinucleotides, is a persistent epigenetic process that controls cell type-specific gene expression. As a result, DNA methylation patterns in many genomic regions change between cell types. The gold standard for studying DNA methylation is whole genome bisulfite sequencing (WGBS), which enables single-nucleotide precision at all cytosines in the genome. The mean methylation level at each cytosine is normally reported, but in bulk tissues made up of numerous cell types, this value is a weighted average of all cells in the sample, masking cell type-specific variances. However, single-cell WGBS solves this problem.

Rationale of whole genome bisulfite sequencing.Fig.1. Rationale of whole genome bisulfite sequencing. (Scott, 2020)

Single Cell Reduced Representation Bisulfite Sequencing Workflow

To handle huge quantities of samples, Creative Biolabs has developed a rapid and cost-effective single-cell whole genome bisulfite sequencing method. Single cell isolation, bisulfite conversion, library creation, and next-generation sequencing are all included in our one-stop solution. For single-cell whole genome bisulfite sequencing, we also offer data analysis services such as alignment and methylation status calling at both single CpG and regional resolutions.

Workflow of single-cell whole genome bisulfite sequencing.Fig.2. Workflow of single-cell whole genome bisulfite sequencing.

Features of Single-cell Whole Genome Bisulfite Sequencing

  • Across the whole genome, more than 90% of CpG loci have been covered.
  • Accurately measure 5mC across single-cell genomes.
  • Flexible enough to map DNA methylation in single cells and extremely tiny cell populations.

Our Advantages

  • Skillful scientific team: we will provide outstanding technical support for your research, which will be prompted by a large number of scientific publications as well as our in-house experience.
  • Unrivaled data quality: we promise that more than 80% of bases will have a Q30 quality score, which is higher than Illumina's official guarantee of 75%.
  • Comprehensive data analysis: For mapping, DMR analysis, functional analysis, and data visualization, we employ widely-accepted mainstream tools such as Bismark and a mature in-house pipeline, providing you with both standard and customized bioinformatics investigations.

Results Display & Published Data

Paper Title Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
Journal Nature methods
IF 28.547
Published 2014
Abstract They present a single-cell bisulfite sequencing (scBS-seq) approach for measuring DNA methylation at up to 48.4% of CpG sites with high accuracy. Epigenetic heterogeneity was seen in embryonic stem cells maintained in serum or 2i medium, with '2i-like' cells present in serum culture. The full DNA methylome was largely recapitulated by combining 12 unique mouse oocyte datasets, making scBS-seq a versatile method for investigating DNA methylation in rare cells and heterogeneous populations.

(A) Estimated DNA methylation rates in an example region comprising the Nanog gene and some annotated characteristics using a sliding window. Dot size indicates the inverse of estimating error, and each ESC is represented by a distinct color (bottom).
(B) Genome-wide cluster dendrogram and distance matrix based on estimated methylation rates for all ESCs and bulk samples.
(C) Methylation rates of the top 300 most variable locations in single-cell ESC samples are depicted as a heatmap. Sample dendrograms (left) and site dendrograms (right) are shown. The average methylation rate over the entire genome is displayed in the left track ('all').
(D) The diversity of locations in distinct genomic settings. The interquartile range with the median is represented by boxes; whiskers equate to 1.5 times the interquartile range. The interquartile range for all genome-wide sites is represented by the shaded gray zone.

scBS-seq reveals DNA methylation heterogeneity in ESCs.Fig.3. scBS-seq reveals DNA methylation heterogeneity in ESCs. (Smallwood, 2014)

Paper Title Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells
Journal Cell stem cell
IF 24.633
Published 2013
Abstract The use of two kinase inhibitors (2i) allows for the pluripotent ground state derivation of mouse embryonic stem cells (ESCs). They reveal that male 2i ESCs are universally hypomethylated when compared to conventional ESCs maintained in blood using whole-genome bisulfite sequencing (WGBS). Female ESCs are hypomethyated in serum in the same way as male ESCs are, and DNA methylation is lowered even more in 2i.

(A) Mass spectrometry of total 5mC (left) or 5hmC (right) (MS).
(B) REX1-positive and -negative populations within Rex/GFP-serum ESCs at 5mC and 5hmC.
(C) Immunohistochemistry of E14 serum and E14 2i-adapted ESCs at 5mC and 5hmC.
(D) 5mC and 5hmC in EpiSCs.
(E) WGBS total 5(h)mC. A prior work provided the WGBS profile of "159-2" ESCs.
(F) WGBS distribution of 5(h)mC levels in the context of a CpG sequence. The Tukey five-number summary is used to create the boxplot layout.
(G) A typical example depicting methylation profiles of the various ESCs.
(H) Genome-wide distribution of DNA methylation levels for individual CpGs.
(I) Smoothed scatter plot between DNA methylation levels of individual CpGs genome-wide.
(J) Averaged methylation profiles over various functional genomic elements as characterized in E14 serum.

Data analysis of scWGBS-seq.Fig.4. Genome distribution of CpGs captured by RRBS. (Kim, 2018)

Please contact us for more details about our single cell whole-genome bisulfite sequencing service. Our experts will help design an optimal solution for your project and trouble-shoot for you throughout the whole process.


  1. Scott, C.A., et al. Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data. Genome biology. 2020; 21(1): 1-23.
  2. Smallwood, S.A., et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nature methods. 2014; 11(8): 817-820.
  3. Habibi, E., et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell stem cell. 2013; 13(3): 360-369.
! ! For Research Use Only. Not for diagnostic or therapeutic purposes.