TABLE 2.
Performance in data quality and coverage achieved by the single-cell multiomics techniques reviewed.
| Method | Genome data | Transcriptome data | DNA methylome data | ||||
|---|---|---|---|---|---|---|---|
| Coverage (# of accessible regions captured per cell) | Mapping rate | Gene detection rate | Exon mapping rate | Mapping rate | Coverage (# of CpGs captured per cell) | Mapping rate | |
| scCAT-seq | 210,000 uniquely mapped fragments/cell | 67% | 8,725 (human) | 54.9% | |||
| Paired-seq | 2,114 unique reads/nucleus; 1,367 ATAC fragments in peaks | - | 1,481 unique reads/nucleus; 726 UMIs (mouse) | - | - | ||
| sc(ATAC + RNA)-seq | 1,000–10,000 unique fragments/cell; 40–65% map to peaks | - | 1,500–3,000 genes/cell (human) | 1.6% | 61% | ||
| sci-CAR | 1,456 unique reads; 915 ATAC fragments in peaks | - | 3,276 UMIs (mouse) | - | - | ||
| SNARE-seq | 2,720/nucleus; 1,059 ATAC fragments in peaks | 91% | 623 UMIs (mouse) | 37% | 94% | ||
| ASTAR-seq | 142,886 library size; 27.9% fragments in peaks | 86% | >15% (9,739) (human) | >75% | 73.8% | ||
| SHARE-seq | 7,805 ATAC fragments in peaks; 65.5% fragments in peaks | - | 9,290 UMIs (mouse) | - | - | ||
| ISSAAC-seq | 58,000 unique reads in peaks; 37% fragments in peaks | >17,000 UMIs (mouse); >4,000 genes (mouse) | 35–60% | ||||
| scDam&T-seq | - | - | 2,282 genes (mouse) | - | - | ||
| scNOMe-seq | 6.7 million GpCs/cell; 20,388 DHSs | 52% | 1.3 million CpGs/cell | - | |||
| scCOOL-seq | 2,800 NDRs/cell; 19.7 million GCH; aggregate: 77.2% | 22% | 2.2 million WCGs (10.1%); agg.: 67.4% | - | |||
| iscCOOL-seq | Aggregate: 84.7% of GCH | 62% | Aggregate: >80% of CpG sites | - | |||
| scMethyl-HiC | 80,763 informative contacts per nucleus (150 cells) | - | 567,380 CpGs/nucleus | - | |||
| sn-m3C-seq | 500,000 contacts/cell (4,200 cells) | - | 27.5% of mouse genome | 72% | |||
| scNMT-seq | 15% of GpCs; 75% of promoters, 85% of gene bodies probed | - | - | - | - | 22.8% of mouse genome | 32% |
| scNOMeRe-seq | 31 million GCH; 15.5% per cell | - | 10,000–15,000 genes (mouse) | - | - | 3.49 million WCG (15.8%) | - |
| scSIDR-seq | - | >90% | 5,690 genes (human) | 87% | - | ||
| TARGET-seq | Detected all mutations in 98.4% of cells | - | 8,200 genes (human) | - | - | ||
| RETrace | 1,217 microsatellites/cell | - | 146,000 CpGs/cell | - | |||
| scTrio-seq | - | 8,106 genes (human) | - | - | 16.4 million CpGs/cell | - | |
Grey blocks = molecular layer not profiled by the technique. - = molecular layer is profiled by the technique, but data is not provided. The methylation status of GCH, sites (GCA/GCT/GCC) is used to analyze chromatin accessibility, while the methylation status of WCG, sites (ACG/TCG) is used to analyze the endogenous DNA, methylation.