. Author manuscript; available in PMC: 2021 Dec 15.

Published in final edited form as: Nat Protoc. 2021 Jul 9;16(8):4004–4030. doi: 10.1038/s41596-021-00571-9

Table 1 ∣.

Comparison of methods for profiling the methylome and transcriptome of single cells

	Smart-RRBS	scM&T-seq²³	scTrio-seq²⁷	scMT-seq²⁴
Cell-isolation technique	FACS or manual isolation	FACS or manual isolation	Manual isolation	Manual isolation
Separation of mRNA and genomic DNA	Dynabeads M-280 streptavidin	Dynabeads MyOne streptavidin C1	Manual isolation of nucleus	Manual isolation of nucleus
Batch size (single cells)	96–192	96	Dozens	Dozens
Protocol for methylome	Msc-RRBS⁹	scBS-seq¹²	sc-RRBS⁴⁴	sc-RRBS⁴⁴
Protocol for transcriptome	Smart-seq2²⁸	Smart-seq2²⁸	mRNA-seq¹	Smart-seq2²⁸
CpGs covered per cell (million)	1.4^a	2.5^b	1.5^c	0.5^d
Fraction of CpGs covered (%)	5^a	9^b	5^c	2^d

MspI+HaeIII digest; mean of 2.2 million reads per cell; this paper.

Mean of 11.6 million reads per cell; ref. ²³.

MspI digest; mean of 20.8 million reads per cell; ref. ²⁷.

Mouse cells; MspI digest; mean of 6.7 million reads per cell; ref. ²⁴.