Table 1.
Comparison of common single cell flow cytometry technologies by probe type
| Mass cytometry | Fluorescence cytometry | Single cell poly-A RNA-seq | |
|---|---|---|---|
| Detection method | Time-of-flight of ionized heavy elemental isotopes | Emitted light and light scatter | Nucleic acid sequence |
| Example probes | Metal-conjugated antibodies, metal-conjugated small molecules | Fluorochrome-conjugated antibodies, fluorescent molecules | Poly-A targeted oligonucleotides, antibody-conjugated oligonucleotides [144] |
| Example cellular features and targets measured | Proteins, phospho-proteins, chromatin modifications [124], RNA transcripts [131–133], platinum drug uptake [128, 129], cell cycle status and DNA synthesis [130], cell size [125], apoptosis [48], and viability [27] | Proteins, phospho-proteins, chromatin modifications [145], RNA transcripts [146], fluorescent drug uptake [147], metabolism and redox state [148, 149], cell cycle status and DNA synthesis [150], cell size and granularity, apoptosis [151] and viability [152] | Poly-adenylated RNA transcripts, CITE-seq probes [144] |
| Minimum cells per sample needed at start of protocol | 50 000 cells | 50 000 cells | 200 cells [153]a |
| Cell capture rate | 30–60% [31, 32] | > 95% | 5–65% [154] |
| Target capture | > 95% | > 95% | 10–40% [154–156] |
| Example of analyzed cell events per study | 2 000 000 cells per study | 20 000 000 cells per study | 5000 cells per study [157] |
| Resolution, arcsinh (max / error)b | ~6-9 e.g., arcsinh(12,000/5) | ~5-9 e.g., arcsinh(262, 144/150), arcsinh(4,194,300/6,000)c | ~2-3 e.g., arcsinh(10/1) |
| Cell throughput | Up to 104 cells·s–1 [33] | Up to 105 cells·s–1 [31] | Up to 104 cells·s–1 [155] |
| Features/available channels | 50/200 channels | 30/64 channelsc | ~ 30 000/N/A |
| Degree of crosstalk between parameters | 3% (range: 0–8.6%) [55] | 19.5% (4.9–51.1%) [56] | N/A |
| Accessibility | Major research institutions | > 20 features: major research institutions; ~ 4 color common | Major research institutions |
| Total cost | $0.004-$0.01/cell [31] | < $0.001/cell | $0.05-$3.00/cell [158] |
a
Number calculated based on 10 assumed number of cell types, rarest cell type makes up 10%, and at least 10 cells are desired per cell type; see reference for a sample size calculator.
b
Max is an example maximum range of the instrument scale; error is the typical error for that scale.
c
Includes capabilities of novel instruments such as Cytek™ Aurora (Cytek Biosciences), ZE5™ (Bio-Rad), and FACSymphony™ (BD)