Single-cell and spatial omics methods
| Source material . | Method . | Technologiesa . | Data type . | Advantages . | Limitations . |
|---|---|---|---|---|---|
| Dissociated tissue | Plate-based sequencing | Smart-Seq2 | mRNA | Generate full-length transcripts, allow detection of genes that are not highly expressed and other rare transcripts | Limited by plate size and the quantity of cells available for analysis |
| Droplet-based microfluidics sequencing | 10X Genomics 3′ scRNA-seq | mRNA | Higher throughput (thousands of cells), easy to multiplex | Only from the 5′ or 3′ end of the transcript, omitting the detection of allele-specific expression and other isoforms | |
| 10X Genomics 5′ scRNA-seq + scTCR-seq | mRNA, T cell receptor clonotype | ||||
| CITE-seq | mRNA, protein | ||||
| scATAC-seq (10X Genomics Multiome) | mRNA, chromatin accessibility | ||||
| Tissue section | Microarray-based sequencing | 10X Genomics Visium | Spatial, mRNA (55 μm) | Unbiased, probes include 18,000 unique genes | Low capture efficiency, low resolution |
| Imaging-based | Phenocycler (CODEX) | Spatial, protein (subcellular resolution, DNA oligo-tagged antibodies) | High resolution (single cell and subcelluar), retains information on physical interactions within and between cells, quantitatively characterizes protein expression | Readout limited to targeted markers (14 for RareCyte, 50–60 for CODEX and IBEX), iterations needed to collect multiple markers, antibody validation needed | |
| IBEX | Spatial, protein (subcellular resolution, flurochrome-tagged antibodies) | ||||
| RareCyte | Spatial, protein (subcellular resolution, flurochrome-tagged antibodies) |
| Source material . | Method . | Technologiesa . | Data type . | Advantages . | Limitations . |
|---|---|---|---|---|---|
| Dissociated tissue | Plate-based sequencing | Smart-Seq2 | mRNA | Generate full-length transcripts, allow detection of genes that are not highly expressed and other rare transcripts | Limited by plate size and the quantity of cells available for analysis |
| Droplet-based microfluidics sequencing | 10X Genomics 3′ scRNA-seq | mRNA | Higher throughput (thousands of cells), easy to multiplex | Only from the 5′ or 3′ end of the transcript, omitting the detection of allele-specific expression and other isoforms | |
| 10X Genomics 5′ scRNA-seq + scTCR-seq | mRNA, T cell receptor clonotype | ||||
| CITE-seq | mRNA, protein | ||||
| scATAC-seq (10X Genomics Multiome) | mRNA, chromatin accessibility | ||||
| Tissue section | Microarray-based sequencing | 10X Genomics Visium | Spatial, mRNA (55 μm) | Unbiased, probes include 18,000 unique genes | Low capture efficiency, low resolution |
| Imaging-based | Phenocycler (CODEX) | Spatial, protein (subcellular resolution, DNA oligo-tagged antibodies) | High resolution (single cell and subcelluar), retains information on physical interactions within and between cells, quantitatively characterizes protein expression | Readout limited to targeted markers (14 for RareCyte, 50–60 for CODEX and IBEX), iterations needed to collect multiple markers, antibody validation needed | |
| IBEX | Spatial, protein (subcellular resolution, flurochrome-tagged antibodies) | ||||
| RareCyte | Spatial, protein (subcellular resolution, flurochrome-tagged antibodies) |
Non exhaustive list, limited to technologies used in the cited literature.