Table 2 |.
Comparison of array-based spatial transcriptomic methods
| ST method | DNA features | Barcode sequencing on each array | Feature diameter(s) (μm) | Feature center distance(s) (μm) | Percentage of array area covered by featuresa | Feature density (features per mm2) | Array substrate | Tissue used for RNA capturingb | cDNA synthesis and amplification | Mean UMIsc | Dataset |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Visium | Spotted DNA | No | 55 | 100 | 27% | ~110 | Glass | Mouse OB, 10 μm thick, tissue fixation and permeabilization | TSO and PCR | 15,377/55 μm | GSE153859 (ref. 106) |
| DBiT-seq | Microfluidic wells | No | (1) 10 (2) 25 (3) 50 |
(1) 30 (2) 53 (3) 100 |
(1) 11% (2) 22% (3) 25% |
(1) 1,100 (2) 360 (3) 100 |
PDMS | Mouse embryo, 7 μm thick, tissue fixation and permeabilization | TSO and PCR | ~5,000/10 μm | GSE137986 (ref. 57) |
| Slide-seqV2 | Assembled beads | Yes | 10 | 10 | 78% | 1×104 | Glass | Mouse OB, 10 μm thick, freshly frozen | TSO and PCR | 497/10 μm | (ref. 107) |
| HDST | Assembled beads | Yes | 2 | 3 | 34% | 1.07×105 | Silicon | Mouse OB, 10 μm thick, tissue fixation and permeabilization | TSO and PCR | 12/10 μm or 2/2 μm | GSE130682 (ref. 108) |
| Seq-Scope | Illumina DNA clusters | Yes | ≥0.5 | ≤0.8 | ≤70% | ≤1.5×106 | Linear PAA coating | Mouse colon, 10 μm thick, tissue fixation and permeabilization | RPE and PCR | ~2,743/10 μm | GSE169706 (ref. 61) |
| Stereo-seq | DNA nanoballs | Yes | 0.22 | (1) 0.5 (2) 0.715 | (1) 15% (2) 7% | (1) 4×106 (2) 1.96×106 | Silicon | Mouse OB, 10 μm thick, tissue fixation and permeabilization | TSO and PCR | ~1,450/10 μm or 59/2 μm | GSE153164 (ref. 62) |
| PIXEL-seq | Polonies | No | ~1 | ~1 | >90% | ≤1×106 | Cross-linked PAA gel | Mouse OB, 10 μm thick, freshly frozen | TSO and PCR | 977/10 μm or 47/2 μm | GSE186097 (ref. 64) |
HDST, high-definition spatial transcriptomics; OB, olfactory bulb; PAA, polyacrylamide; PDMS, polydimethylsiloxane; RPE, random priming and extension; ST, spatial transcriptomic; TSO, template-switching oligonucleotide.
The percentages for Visium, DBiT-seq, Slide-seqV2, HDST and Stereo-seq were calculated based on reported feature sizes, densities and spatial patterns. The percentage for Seq-Scope was measured by analyzing a reported cluster image of the flow cell hybridized with the highest template concentration, 100 pM.
Different RNA-capturing conditions were used, and some probably captured RNA from multiple cell layers from a whole tissue section. Different amplification methods have different yields. Multiple-displacement amplification amplifies cDNA fragments and typically gives a higher yield than PCR amplification of full-length cDNA.
Unique molecular identifier (UMI) counts were obtained from the original publications. Feature gaps typically were not considered in the calculations.