Table 1 Overview of spatial multi-omics methods. Experimental methods, corresponding instruments, analyte principles, modalities, feature scale, and resolution are shown for each category. The cost row offers an estimation on the price per sample and does not include initial investment into the device
From: Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases
| Â | NGS based multi-omics | Imaging based multi-omics | MS- based multi-omics | ||||||
|---|---|---|---|---|---|---|---|---|---|
|  | Spatial non-deterministic barcoding | Spatial deterministic barcoding | ISS | Multiplex ISH – diffraction limited | Multiplex ISH – non diffraction limited | Cyclic IF | Ion-labelled antibodies | microdissection | |
Method | Visium35,36, Slide-SeqV237,38, STEREO-Seq101, HDST39 | DBiT-Seq53 | HybISS92, FISSEQ, | MERFISH93, seqFISH94, osmFISH, EEL-FISH, | FLASH-PAINT103, DNA-PAINT, SUM-PAINT104 | CODEX72, COMET, 4i70, IBEX71, Immuno-SABER73 | IMC68, MIBI69 | Deep Visual Proteomics77,78 (DVP) | |
Instrument | Sequencer (short/long read) | Sequencer (short/long read) | microscope (epifluorescence confocal) | microscope (epifluorescence confocal) | microscope (confocal, TIRF, STED) | microscope | Mass-Spec | Laser-microdissection microscope + Mass-Spec | |
Analyte principles | Barcoded primer | Barcoded primer | Padlock probes | Probe panel | Oligo-labeled nanobodies | Oligo or IF labeled antibodies | Ion-labeled antibodies | Tissues markers and AI software for dissection | |
Modalities | DNA, RNA, protein | DNA, RNA, protein | DNA, RNA | DNA, RNA, protein | RNA, protein | protein | protein | protein | |
Feature scale | 10.000s Protein: 100a | RNA:10.000s Protein: 100s | 1000s | cells (1000s) tissues (100s) | 12 (theoretically 10.000s) | 1-200 | 1-50 | unlimited | |
Resolution | 1-55 µm, Stereo-seq: 200 nm | 10 µm | Diffraction limited | Diffraction limited | Sub-5 nm | Diffraction limited | 100 nm-1µm | 5-10 µm (cellular level) | |
Costs | +++ | ++ | ++++ | ++++ | + | + - ++ | ++ | ++ | |