TABLE 1.

Summary of reviewed single-cell multiomics methods.

Method	Molecular layers profiled					Throughput (low/medium/high)	Special features (compared to techniques from same category)	Format	References
	Epigenome			Genome	Transcriptome
	Chromatin accessibility	Chromatin conformation	DNAme	CNVs/ploidy/microsatellites/mutation	poly(A)+ RNA
scCAT-seq	x				x	+	⇑ usable fragments	well	Liu et al. (2019)
Paired-seq	x				x	+++	⇑ throughput	well	Zhu et al. (2019)
sc(ATAC + RNA)-seq	x				x	+	⇓ cost; simple workflow	well	Reyes et al. (2019a)
sci-CAR	x				x	+++	⇑ acc. & RNA intersect coverage	well	Cao et al. (2018)
SNARE-seq	x				x	+++	⇑ sensitivity	droplet	Chen et al. (2019)
ASTAR-seq	x				x	++	⇓ price-performance ratio	microfluidics	Xing et al. (2020)
SHARE-seq	x				x	+++	⇑ throughput, performance	well	Ma Sai. et al. (2020)
ISSAAC-seq	x				x	+++	⇑ throughput, performance (esp. ATAC)	well/droplet	Xu et al. (2022)
scDam&T-seq		x			x	+	protein-DNA interactions information	well	Rooijers et al. (2019)
scNOMe-seq	x		x			+	estimates nucleosome phasing	well	Pott, (2017)
scCOOL-seq	x		x	x		+	⇑ acc. & DNAme intersect coverage	well	Guo et al. (2017)
iscCOOL-seq	x		x			++	⇑ accessibility coverage	well	Gu et al. (2019a)
scMethyl-HiC		x	x			+	⇑ mapping rate	well	Li et al. (2019)
sn-m3C-seq		x	x			+++	⇑ DNAme coverage	well	Lee et al. (2019)
scNMT-seq	x		x		x	++	⇑ throughput	well	Clark et al. (2018)
scNOMeRe-seq	x		x		x	+	⇑ DNAme coverage	well	Wang et al. (2021)
scSIDR-seq				x	x	+	captures total RNA	well	Han et al. (2018)
TARGET-seq				x	x	+++	⇓ cost; ⇑ throughput	well	Rodriguez-Meira et al. (2019)
RETrace			x	x		+	captures microsatellites	well	Wei and Zhang, (2020)
scTrio-seq2			x	x	x	++	⇑ DNAme coverage	well	Bian et al. (2018)

Throughput: + <500 cells, ++ <2000 cells, +++ >2000 cells. acc. = (chromatin) accessibility. scCAT-seq, single-cell chromatin accessibility and transcriptome sequencing), Paired-seq - parallel analysis of individual cells for RNA, expression and DNA, accessibility by sequencing, sc(ATAC + RNA)-seq - simultaneous chromatin accessibility and gene expression profiling, sci-CAR, single-cell combinatorial indexing-based chromatin accessibility and RNA, SNARE-seq, single-nucleus chromatin accessibility and mRNA, expression profiling; ASTAR-seq, assay for single-cell transcriptome and accessibility regions; SHARE-seq, simultaneous high-throughput ATAC, and RNA, expression with sequencing in single cells; ISSAAC-seq, in situ SHERRY, after ATAC-seq, scDam&T-seq - single-cell DNA, adenine methyltransferase identification (DamID) and messenger RNA, sequencing, scNOMe-seq - single-cell nucleosome occupancy and methylome-sequencing, scCOOL-seq, single-cell chromatin overall omic-scale landscape sequencing, iscCOOL-seq, improved single-cell chromatin overall omic-scale landscape sequencing; scMethyl-HiC, single-cell DNA, methylation and chromatin conformation capture, sn-m3C-seq - single-nucleus methyl-chromatin conformation capture sequencing, scNMT-seq, single-cell nucleosome, methylation and transcription sequencing, scNOMeRe-seq - single-cell nucleosome occupancy, methylome and RNA, expression sequencing; scSIDR-seq, simultaneous isolation and sequencing of genomic DNA, and total RNA, TARGET-seq, single-cell targeted mutational analysis and parallel RNA, sequencing, RETrace - simultaneous retrospective lineage tracing and methylation profiling of single cells, scTrio-seq - single-cell triple omics sequencing.