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. Author manuscript; available in PMC: 2023 Apr 1.
Published in final edited form as: J Invest Dermatol. 2022 Apr;142(4):993–1001.e1. doi: 10.1016/j.jid.2021.12.014

Table 2.

Comparison of ST Technologies

Category Resolution Capture Approach Number of Unique Genes Assayed (Multiplex Capacity) Advantages Limitations
merFISH ISH Subcellular Targeted Up to 500 Up to 10,000*

  • Subcellular resolution

  • High RNA capture efficiency

  • Requires specialized equipment

  • Cost and labor increase with number of targeted readouts

  • Readout limited to RNA targets
seqFISH ISH Subcellular Targeted Up to 249

  • Subcellular resolution

  • High RNA capture efficiency

  • Requires specialized equipment

  • Cost and labor increase with number of targeted readouts

  • Readout limited to RNA targets
seqFISH+ ISH Subcellular Targeted Up to 10,000

  • Subcellular resolution

  • High RNA capture efficiency

  • Requires specialized equipment

  • Cost and labor increase with number of targeted readouts

  • Readout limited to RNA targets
Barcoded Padlock Probe ISS ISS Subcellular Targeted Up to 100

  • Subcellular resolution

  • Limited fields of view

  • Readout limited to RNA targets

  • Lower multiplex capacity than other ISS
FISSEQ ISS Subcellular Unbiased Whole transcriptome

  • Subcellular resolution

  • Unbiased readout of whole

  • transcriptome

  • Low capture efficiency

  • Difficult to reproduce outside of originators’ lab
STARmap ISS Subcellular Targeted Up to 1,000

  • Subcellular resolution

  • Increased sensitivity

  • High RNA capture efficiency

  • 3D localization

  • Limited fields of view

  • Readout limited to RNA targets

  • Difficult to reproduce outside of originators’ lab
10X Visium ISC 55 μm-diameter capture spots Unbiased Whole transcriptome

  • Unbiased readout of whole transcriptome

  • Little specialized equipment required

  • Low capture efficiency

  • Low resolution compared to ISH/ISS
Slide-seq ISC 10 μm-diameter capture spots Unbiased Whole transcriptome

  • Unbiased readout of whole transcriptome

  • Improved resolution from 10X Visium

  • Low capture efficiency

  • Low resolution compared to ISH/ISS
Seq-Scope ISC ~0.6 μm-diameter capture spots (subcellular) Unbiased Whole transcriptome

  • Unbiased readout of whole transcriptome

  • Improved resolution and efficiency from 10X Visium and Slide-seq

  • Small field of view

  • Technical challenges associated with repurposing of Illumina flow cell
*

Demonstrated exclusively in cultured cells; all values lacking an asterisk indicate validation in intact tissue samples