The scMT-seq method was published by Hu et al. in Genome Biology 17, 88. This should not to be confused with scM&T-seq. The scMT-seq physically separates nuclei and the cytopalsm. The mRNA is in cytoplasm and SMART-seq2 method was used for scRNA-seq, click here to see the step-by-step protocol; the genomic DNA is in the nuclei, scRRBS method was used to profile methylation, and click here to see the step-by-step protocol.