Table 1.
Advantages and limitations of the single-cell and spatial transcriptomic approaches
| Advantages | Limitations | |
|---|---|---|
| Single cell RNA-seq | 1) Profile three-dimensional samples 2) Single-cell resolution 3) High gene detection sensitivity (5%–40%a) |
1) Cell wall digestion variation may cause cell-type bias 2) Extra-large cell may block the emulsion process 3) Difficult to identify cell clusters due to lack of known markers in most plant species |
| Spatial transcriptomics: Visium | 1) Spatially resolved transcriptome profiling 2) Good RNA integrity 3) Cell size is not a limiting factor 4) High gene detection sensitivity (>6.9%a) |
1) Profile two-dimensional sections 2) Low resolution (five to 10 cells) |
| Spatial transcriptomics: Slide-seq and Stereo-seq | 1) Spatially resolved transcriptome profiling 2) Good RNA integrity 3) Cell size is not a limiting factor 4) High resolution (single cell or subcellular) |
1) Profile two-dimensional sections 2) Low gene detection sensitivity (0.3%a) |
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aThe gene detection sensitivity is defined as the percentage of detected unique transcripts relative to the total number of unique transcripts in a particular area. Data are from Asp et al. (2020).
