Table 2 Comparison of ST seq technologies
Method name | Year | Resolution | Sample | Information | Pros/Cons |
|---|---|---|---|---|---|
Microdissection-based | |||||
1996 | ROI | FF/FFPE | Transcriptome/Target | Robust/Low throughput | |
tomo-seq [36] | 2014 | 3D tissue | FF | Transcriptome | 3D constructable/Multiple identical biological samples are required |
TIVA [37] | 2014 | single cell | Fresh cells | Transcriptome | Can be applied to live cells/Low throughput |
Geo-seq [35] | 2017 | 10 cells | FF | Transcriptome | Extended version of the LCM/Low throughput |
NICHE-seq [38] | 2017 | ROI | Fresh cells | Transcriptome | Can be applied to live cells/Lost spatial information within the region of interest |
ProximID [39] | 2018 | 2–3 cells | Fresh cells | Transcriptome | Reflects the physical relationship between cells/Low throughput |
In situ hybridization-based | |||||
RNA-ISH [40] | late 1970 | Subcellular | Ethanole fixes | gene | High sensitivity/Low throughput |
smFISH [41] | 2008 | Subcellular | FF/FFPE | Target (some gene) | High sensitivity/Low throughput |
seqFISH [42] | 2014 | Subcellular | FF | Target (12gene) | Multiplex/Small observation area, not single molecular |
MERFISH [43] | 2015 | Subcellular | FF | Target (1001gene) | Multiplex/Small observation area, not single molecular |
seqFISH+ [44] | 2019 | Subcellular | FF | Target (10000gene) | Highly multiplex, resolution/Small observation area, High cost |
In situ sequencing-based | |||||
padlock-based ISS technology [46] | 2013 | Subcellular | FF/FFPE | Target (~ 100gene) | Can detect SNVs/limited gene number |
FISSEQ [49] | 2014 | Subcellular | FF/FFPE | Transcriptome | Non target/Small observation area |
BaristaSeq [48] | 2018 | Subcellular | cell line | Target | Can detect SNVs/Target sequence is necessary |
STARmap [45] | 2018 | Subcellular | Fresh cell/FF | Target (1024gene) | Avoiding RTstep, 3D constructable/Small observation area |
HybISS [47] | 2020 | Subcellular | FF | Target | Improved version of the padlock-based ISS technology/Small observation area |
In situ capturing-based | |||||
Spatial Transcriptome [50] | 2016 | 20–100 cells | FF | Transcriptome | Whole transcriptome, Wide observation area/not single cell resolution |
Slide-seq [51] | 2019 | Single cell (10um) | FF | Transcriptome | High resolution/Low sensitivity |
HDST [52] | 2019 | Single cell (2um) | FF | Transcriptome | High resolution/Low sensitivity |
Digital Spatial Profiling [53] | 2020 | ROI (1-5000cell) | FFPE | Target (~ 5000 gene) | Compatible with FFPE/Small observation area |