Table 2.

Single-cell multi-omics sequencing for spatial information profiling together with their specific applications, results and data sources

Method	Data source	Molecular layers	Objective and outcome(s)	Platform(s)
MERFISH [28]	GSE67685	Copy numbers and spatial distributions of a large number of RNA species within single cells.	To overcome the obstacle of a limited number of RNA species that can be simultaneously imaged in individual cells. Thousands of RNA species could be imaged in single cells.	Illumina MiSeq
Moffitt et al. [29]	GSE113576	Profiled about 31 000 cells using scRNA-seq and imaged about 1.1 million cells within intact tissues using MERFISH.	To identify molecularly distinct cell types and map their spatial and functional organization in the tissue. A combination MERFISH with scRNA-seq revealed the molecular, spatial and functional organization of neurons within the hypothalamic preoptic region.	Illumina NextSeq 500
osmFISH [30]	http://linnarssonlab.org/osmFISH	Spatially resolved single-cell transcriptomics profiling.	To use spatial information and detect a large number of cell type–specific markers simultaneously in large tissue. The spatial information inherent to osmFISH could improve the interpretation of expression profiles.	N/A
seqFISH [31]	N/A	In situ profiling and visualization of transcription at the single-cell level.	To reveal spatial and temporal features of transcriptome. The sequential barcoding method enabled the transcriptome to be directly imaged at single-cell resolution in complex samples such as brain tissue.	N/A
seqFISH+ [32]	GSE98674	Superresolution imaging and multiplexing of 10 000 genes in a single cell.	To overcome the optical crowding problem during implementation of spatial profiling experiments. With the genome coverage and spatial resolution of seqFISH+, it was possible to perform discovery-driven studies directly in situ.	Illumina HiSeq 2500
FISSEQ [33]	http://arep.med.harv ard.edu/FISSEQ_Science:2014/	Transcriptome-wide RNA sequencing with 8102 genes in situ in human primary fibroblasts with a simulated wound-healing assay.	To demonstrate imaging and analytic approaches across multiple specimen types and spatial scales. FISSEQ predominantly detected genes characterizing cell type and function.	Illumina humanRef–8 v2.0 expression beadchip,Harvard_Human _BeadChip_23K_Ref8v3, Illumina HiSeq 2000
ST [34]	N/A	Quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections.	To introduce positional molecular barcodes in the complementary DNA synthesis reaction in an intact tissue section before RNA-seq. ST revealed unexpected heterogeneity within a biopsy, which would not be possible to detect with regular transcriptome analysis and which may give more detailed prognostic information.	N/A
Visium Spatial Technology	https://www.10xgeno mics.com/products/ spatial–gene– expression	The whole transcriptome with morphological context within tissue sections.	To discover novel insights into normal development, disease pathology and clinical translational research.	Visium platform
Slide-seq [35]	https://portals.broad institute.org/single_cell/study/slide--seq –study	Spatially resolved gene expression data from individual cells.	To develop a high-throughput, genome-wide readout of gene expression within cellular resolution Slide-seq was easily integrated with large-scale scRNA-seq datasets and facilitated discovery of spatially defined gene expression patterns in normal and diseased tissues.	N/A
HDST [36]	GSE130682	Transcript coupled spatial barcodes.	To develop high-resolution methods to capture both spatial and molecular characteristics for tissue function. Relating histopathology and transcriptional profiles could help improve understanding of disease biology, and patient diagnosis and treatment.	Illumina NextSeq 500
STARmap [37]	www.starmapre sources.com	RNA quantity and 3D spatial information with more than 1000 genes over six imaging cycles at the single-cell level in intact tissue.	To uncover the integrated relationship between structure and function in complex biological tissues.	Fluorescent Nissl staining.
DBiT-seq [38]	GSE137986	mRNAs and spatial information coupled with a panel of 22 proteins in mouse embryos tissue slide.	To dissect the initiation of early organogenesis at the whole embryo scale. Deterministic barcoding in tissue enabled NGS-based spatial multi-omics mapping.	Illumina HiSeq 4000
Baccin et al. [39]	GSE122467	Transcriptomics and spatial position information of distinct bone marrow sections at the single-cell level.	To define sources of prohematopoietic factors, infer bone marrow-resident cell types and localize their position. The cellular and spatial organization of bone marrow niches offered a systematic approach to dissect the complex organization of whole organs.	Illumina NextSeq 500