Advances in spatial transcriptomics and related data analysis strategies

Du, Jun; Yang, Yu-Chen; An, Zhi-Jie; Zhang, Ming-Hui; Fu, Xue-Hang; Huang, Zou-Fang; Yuan, Ye; Hou, Jian

doi:10.1186/s12967-023-04150-2

Journal of Translational Medicine

Table 1 Comparisons of Methods and Technologies for Spatial Transcriptomics

From: Advances in spatial transcriptomics and related data analysis strategies

Technique	Year	Sample	Resolution	Genes detected	Strategy	Characteristic	Limitation	References
LCM	1996	Kidney glomeruli, Alzheimer's plaques, in situ breast carcinoma, etc	Cellular	N/A	Microdissection	Faster to perform No contamination to adjacent dissections	Low throughput	[25]
smFISH	1998	Normal rat kidney cells	Subcellular	2	In situ hybridization	Detects single transcripts High sensitivity	Low throughput	[29]
ISS	2013	Human breast cancer	Subcellular	31	In situ sequencing	Based on the padlock probe High accuracy	Needs pre-designed padlock probes	[38]
TIVA	2014	Mouse brain, human brain	Cellular	~ 9000	Spatial barcoding	Capture mRNA from live single cells in vivo	Low throughput	[72]
FISSEQ	2014	Human primary fibroblasts	Subcellular	8102	In situ sequencing	Transcriptome-wide RNA in situ sequencing	Low sequencing depth	[39]
seqFISH	2014	Yeast cells	Subcellular	12	In situ hybridization	Sequential barcoding Enables single-cell-resolution imaging of the transcriptome	Occurrence of errors that may be accumulated	[34]
tomo-seq	2014	Zebrafish embryo	N/A	~ 12,000	Microdissection	High sensitivity High spatial resolution. Construction of transcriptome-wide gene expression atlas in 3D	Several same biological samples needed	[27]
MERFISH	2015	Human fibroblast cells	Subcellular	140	In situ hybridization	Highly multiplexed Capable of detecting and correcting errors	Limited RNA measurement	[35]
smHCR	2016	Zebrafish embryos, mouse brain	Subcellular	5	In situ hybridization	High sensitivity Diffraction-limited resolution	Low throughput	[73]
Spatial Transcriptomics	2016	Adult mouse olfactory bulb	100 μm/55 μm (10 × Genomics Visium)	Entire transcriptome	Spatial barcoding	Provides spatial information	Contains several cells in each sequencing unit	[5]
Geo-seq	2017	Mouse early embryo, mouse brain, etc	10 cells	> 8000	Microdissection	Profiles transcriptomes from several cells while preserving spatial information	Low throughput	[28]
NICHE-seq	2017	Immune cells	Cellular	N/A	Microdissection	Elucidates spatial construction of cell types and corresponding molecular pathways	Limited to genetically engineered models	[74]
BaristaSeq	2018	Baby hamster kidney cells	Subcellular	N/A	In situ sequencing	High efficiency High accuracy	Needs pre-designed padlock probes	[75]
ProximID	2018	Mouse bone marrow	Cellular	N/A	Microdissection	Able to predict preferential associations between cells	Low throughput	[76]
STARmap	2018	Mouse primary visual cortex	Subcellular	160 ~ 1020	In situ sequencing	Able to measure the expression of a single cell in intact tissue High efficiency High accuracy	Low throughput	[42]
osmFISH	2018	Mouse brain	Subcellular	33	In situ hybridization	Automatically delineates tissue regions Able to process large tissue areas	Low throughput	[32]
Slide-seq	2019	Mouse brain	10 μm	Entire transcriptome	Spatial barcoding	High spatial resolution	Low capturing efficiency	[43]
seqFISH +	2019	Mouse brain, fibroblast cells	Subcellular	10,000	In situ hybridization	High accuracy Sub-diffraction-limit resolution	Low throughput	[77]
Nanostring GeoMx DSP	2019	Formalin-fixed, paraffin-embedded patient tissue	10 μm	N/A	Spatial barcoding	High-plex	May create bias in selecting regions	[78]
DNA microscopy	2019	MDA-MB-231 cells, BT-549 cells	Cellular	N/A	In situ sequencing	Able to image biological specimens without optical information Relies on thermodynamic entropy	Empty space causing sparse signals	[79]
APEX-seq	2019	HEK293T cells	Subcellular	N/A	Spatial barcoding	Performed in living cells Allows transcript isoforms with distinct localization to be distinguished	Limited application to human tissue	[80]
HDST	2019	Mouse olfactory bulb	2 μm	Entire transcriptome	Spatial barcoding	High resolution	Data sparsity	[45]
ZipSeq	2020	NIH/3T3 fibroblasts, live lymph node sections, mouse breast cancer	Cellular	Entire transcriptome	Spatial barcoding	Performed on live cells in intact tissues	Limited spatial resolution	[81]
DBiT-seq	2020	Mouse embryos	10 μm	22,969	Spatial barcoding	High spatial resolution Avoid lysis of tissues	Limited flow channels	[82]
ExSeq	2021	Mouse brain, human metastatic breast cancer	Subcellular	3039	In situ sequencing	High spatially precision Highly multiplexed imaging of RNAs in intact cells and tissues	Limits in detecting short transcripts	[40]
Slide-seqV2	2021	Mouse embryos, mouse brain	10 μm	1349	Spatial barcoding	High resolution Higher sensitivity than Slide-seq	May capture transcripts from multiple cells	[44]
XYZeq	2021	Human HEK293T cells, mouse NIH 3T3 cells	500 μm	Entire transcriptome	Spatial barcoding	Enables unbiased single-cell transcriptomic analysis	Requires specialized device	[83]
Seq-Scope	2021	Mouse liver and colon sections	~ 0.5–0.8 μm	Entire transcriptome	Spatial barcoding	High transcriptome capture efficiency Able to visualize the histological organization	Focused on only poly-A transcriptome	[46]
sci-Space	2021	Mouse embryos	200 μm	Entire transcriptome	Spatial barcoding	Retains single-cell resolution while capturing spatial information	Limited spatial resolution	[84]
Stereo-seq	2022	Mouse embryos, adult mouse brain and olfactory bulb	0.22 μm	Entire transcriptome	Spatial barcoding	High resolution High sensitivity Large visualizing field	Limited capturing efficiency	[85]
Ex-ST	2022	Mouse olfactory bulb and hippocampus	20 μm	Entire transcriptome	Spatial barcoding	Uses polyelectrolyte matrices to achieve higher resolution and detection efficiency	May capture transcripts from multiple cells	[86]

smFISH Single-molecule RNA Fluorescence In Situ Hybridization, LCM Laser Capture Microdissection, ISS In Situ Sequencing, TIVA Transcriptome In Vivo Analysis, FISSEQ Fluorescent In Situ RNA Sequencing, seqFISH Sequential Fluorescence In Situ Hybridization, tomo-seq RNA Tomography, MERFISH Multiplexed Error-robust Fluorescence In Situ Hybridization, smHCR Single-molecule Hybridization Chain Reaction, Geo-seq Geographical Position Sequencing, BaristaSeq Barcode In Situ Targeted Sequencing, STARmap Spatially-resolved Transcript Amplicon Readout Mapping, osmFISH Ouroboros Single-molecule RNA Fluorescence In Situ Hybridization. DSP, Digital Spatial Profiling, HDST High-Definition Spatial Transcriptomics, DBiT Deterministic Barcoding in Tissue. ExSeq Expansion Sequencing, Stereo-seq Spatial Enhanced Resolution Omics-sequencing, Ex-ST Expansion Spatial Transcriptomics

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