Single-Cell Methylome and Transcriptome Sequencing

scM&T-seq allows parallel analysis of both epigenetic and gene expression patterns from single cells using Smart-seq2 and scBS-seq (Angermueller et al., 2016). scM&T-Seq is based on G&T-seq, but instead of using MDA for DNA sequencing, it uses scBS-Seq to determine DNA methylation patterns.

Single cells are isolated and individually lysed. The mRNAs are captured with streptavidin-coupled mRNA capture primers to separate them physically from the DNA strands. Smart-seq2 uses RT with template switching and tagmentation to generate cDNA libraries from the mRNA. DNA libraries are prepared via scBS-seq, which involves bisulfite conversion of DNA strands to identify methylated cytosines. Both libraries are ready for sequencing.


  • Investigates links between epigenetic and transcriptional heterogeneity in single cells
  • Because DNA and RNA are physically separated and amplified independently, there is no need to mask coding sequences during analysis


  • Smart-seq2 is not strand-specific and applicable to only poly(A)+ RNA
  • Does not distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC)


Illumina Library prep and Array Kit Selector


Clark S. J., Lee H. J., Smallwood S. A., Kelsey G. and Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016;17:72

Wen L. and Tang F. Single-cell sequencing in stem cell biology. Genome Biol. 2016;17:71


Angermueller C., Clark S. J., Lee H. J., et al. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods. 2016;13:229-232