Main single-cell genomic technologies
| Single-cell approach and assay . | Single-cell applications . | Limitations . | Reference . |
|---|---|---|---|
| Plate based | |||
| FACS | RNA-seq, WGA, DNA methylome, protein analysis | Low number of cells | 63,64,116 |
| Mass cytometry | Protein analysis | Low number of cells; lack of genomic analysis | 68 |
| Micro-well based | |||
| BD Rhapsody (BD Biosciences) | Gene expression (targeted panel or WTA), cell surface marker expression; multiome cell surface expression and gene expression. | 3′ expression only | 117 |
| SMARTer ICELL8 (Takara) | Gene expression: fully automated processing of >1000 individual cells into sequencing-ready libraries; uniform full-length transcript coverage; improved detection of gene fusions; high number of expressed genes | Lower number of cells compared with droplet-based approaches | 118 |
| ATAC-seq | Lower number of cells compared with droplet-based approaches | 119 | |
| Droplet based | |||
| Chromium (10X Genomics) | Gene expression | 3′ or 5′ expression only | 14,69,74,75,86 |
| ATAC-seq | Requires optimization of nuclei isolation; no information on gene expression or mutations | 46 | |
| Immune profiling: full-length V(D)J sequences for paired B-cell or T-cell receptors, cell surface protein expression, antigen specificity, and gene expression, all from a single cell. | 5′ expression only | 90,120,121 | |
| Multiome ATAC+gene expression: simultaneous gene expression and open chromatin from the same cell | Requires optimization of nuclei isolation | 18,122 | |
| Tapestri (Mission Bio) | Identification of CNVs, SNVs, indels, and genome editing sites | Inability to identify gene fusions and structural variations, or novel DNA mutations outside the targeted region | 11-14,66 |
| Single-cell approach and assay . | Single-cell applications . | Limitations . | Reference . |
|---|---|---|---|
| Plate based | |||
| FACS | RNA-seq, WGA, DNA methylome, protein analysis | Low number of cells | 63,64,116 |
| Mass cytometry | Protein analysis | Low number of cells; lack of genomic analysis | 68 |
| Micro-well based | |||
| BD Rhapsody (BD Biosciences) | Gene expression (targeted panel or WTA), cell surface marker expression; multiome cell surface expression and gene expression. | 3′ expression only | 117 |
| SMARTer ICELL8 (Takara) | Gene expression: fully automated processing of >1000 individual cells into sequencing-ready libraries; uniform full-length transcript coverage; improved detection of gene fusions; high number of expressed genes | Lower number of cells compared with droplet-based approaches | 118 |
| ATAC-seq | Lower number of cells compared with droplet-based approaches | 119 | |
| Droplet based | |||
| Chromium (10X Genomics) | Gene expression | 3′ or 5′ expression only | 14,69,74,75,86 |
| ATAC-seq | Requires optimization of nuclei isolation; no information on gene expression or mutations | 46 | |
| Immune profiling: full-length V(D)J sequences for paired B-cell or T-cell receptors, cell surface protein expression, antigen specificity, and gene expression, all from a single cell. | 5′ expression only | 90,120,121 | |
| Multiome ATAC+gene expression: simultaneous gene expression and open chromatin from the same cell | Requires optimization of nuclei isolation | 18,122 | |
| Tapestri (Mission Bio) | Identification of CNVs, SNVs, indels, and genome editing sites | Inability to identify gene fusions and structural variations, or novel DNA mutations outside the targeted region | 11-14,66 |
For each approach applications and limitations are shown.
CNV, copy number variation; FACS, fluorescence-activated cell sorting; SNV, single-nucleotide variation; WGA, whole-genome amplification; WTA, whole-transcriptome amplification.