Table 2.
Overview of commercially available instruments for single-cell collection and analysis.
| Instrument | Chromium System (10x Genomics) | Nadia (Dolomite Bio) | InDrop System (1CellBio) | Illumina Bio-Rad ddSEQ Single-Cell Isolator | Tapestri Platform (MissionBio) | BD Rhapsody Single-Cell Analysis System (BD) | ICELL8 Single-Cell System (Takara) | C1 System and Polaris (Fluidigm) | Puncher Platform (Vycap) | CellRaft AIR System (CellMicrosystems) | DEPArray NxT (Menarini Silicon Biosystems) | AVISO CellCelector (ALS) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Launched in | 10/2016 | 11/2017 | 6/2016 | 1/2017 | 10/2017 | 09/2017 | 10/2015 | 2012 (2015) | 8/2015 | 2017 | 4/2016 | 2006 |
| Principles (Reference) | Droplet-based [89] | Droplet-based (Drop-Seq [84]) | Droplet-base (InDrop-Seq [85]) | Droplet-based | Droplet-based, two-step partitioning [90] | Array of 200,000 microwells, barcoded beads | 5184-well chip, pre-printed barcodes, nano-dispensor [91] | Integrated fluidic circuits for up to 800 cells | Array of 6400 microwells with a pore, filtering, punching needle [92] | Array of 44,000 paramagnetic microwells, punching probe, magnetic collection [93,94] | Microfluidic cartridge with 30,000 dielectrophoretic (DEP) cages [95,96] | Capillary-based [97,98] |
| Main Application | RNA-Seq, DNA-Seq, Immune Repertoire Profiling | RNA-Seq, DroNc-Seq, PACS, open for other | RNA-Seq | RNA-Seq | Targeted DNA-Seq | Targeted RNA-Seq | RNA-Seq | RNA-Seq, DNA-Seq, miRNA-Seq, epigenomics, RT-qPCR | Single-cell collection, rare cell analysis (CTC) | Single-cell collection, tracking cell phenotypes, clonal populations | Single-cell collection, cell–cell interaction | Single-cell collection, transfer of cell colonies |
| Throughput (# of cells analyzed) | High (>10,000) | High (>10,000) | High (>10,000) | High (>10,000) | High (>10,000) | High (>10,000) | Medium (>1000) | Low-medium (48-800) | Low (<100) | Low (<100) | Low (<100) | Low (<100) |
| Visual Control | No | No | No | No | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| Cell Selection | No | No | No | No | No | No | Yes | Yes (C1 size based) | Yes | Yes | Yes | Yes |
| Starting Amount of Cells | High | High | High | High-medium | High | High-medium | Medium | Medium-low | Low | Medium-low | Medium-low | Medium-low |
| Flexibility (Own Protocols) | No | Yes (Nadia Innovate) | Unknown | No | Customize panels | Customize panels | Yes | Yes | Yes | Yes | Yes | Yes |
| Laboratory Skills | Easy | Advanced | Advanced | Easy | Easy | Easy | Easy | Easy | Easy | Easy | Easy | Advanced |
| End-to-End Solution | Yes | No | No | Yes | Yes | Yes | No | Yes | No | No | No | No |
| Extra | Intensive support, 10x Community | Sample chilling, cell and beads stirrer, controllable parameters | Early access program—intensive user support | Product from industry leaders, expertize, scalable (kits for different starting number of cells) | Detect mutation co-occurrence, Characterize rare subclones down to 1% | Automated cell counting, archiving, subsampling, promised upgrade to simultaneous protein-detection | Cell selection combined with high throughput | Automatic workflow, staining, library prep, cell stimulation | Established WGA/WTA protocols using Repli-G kit of Qiagen and the AMPLI-1 kit of Silicon Biosystems | CellRaft System for Inverted Microscopes, QIAscout (Qiagen) | Established WGA/WTA protocols using own kits | Customizable, common labware, various harvest modules |