Spatial transcriptomics: recent developments and insights in respiratory research

Wang, Wen-Jia; Chu, Liu-Xi; He, Li-Yong; Zhang, Ming-Jing; Dang, Kai-Tong; Gao, Chen; Ge, Qin-Yu; Wang, Zhou-Guang; Zhao, Xiang-Wei

doi:10.1186/s40779-023-00471-x

Military Medical Research

Table 2 Single cell multi-omics analysis

From: Spatial transcriptomics: recent developments and insights in respiratory research

Method	Year	Application	Ref.
Transcriptome and genome
G&T-seq	2015	Detection of SNVs and cell chromosome rearrangement	[157]
DR-Seq	2015	DNA copy-number variations within the cancer genome	[158]
SIDR	2018	Copy-number and single-nucleotide variations	[159]
TARGET-seq	2019	The distinct transcriptional signatures of tumor genetic subclones	[160]
DMF-DR-seq	2022	The genome variation-induced abnormal transcriptome expression	[161]
Transcriptome and epigenome
scM&T-seq	2016	Associations between transcriptional and epigenetic variation	[162]
scMT-seq	2016	Correlation between DNA methylation and gene transcription	[163]
scTrio-seq	2016	Epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas	[164]
sc-GEM	2016	Epigenetic variations within and between different cell types	[165]
scNMT-seq	2018	Epigenome interactions during a developmental trajectory	[166]
snDrop-seq and scTHS-seq	2018	Identification of region-specific neuronal and non-neuronal cell types	[167]
sciCAR	2018	Compare the pseudotemporal dynamics of chromatin accessibility	[168]
Paired-seq	2019	Analyze the dynamic and cell-type-specific gene regulatory programs	[169]
SNARE-seq	2019	Reconstruct the transcriptome and epigenetic landscapes of cells	[170]
scCAT-seq	2019	Regulatory relationships between cis-regulatory elements and the target genes	[171]
Transcriptome and proteome
PLAYR	2016	The interplay between transcription and translation	[172]
PEA/STA	2016	Proximity extension assays and complementary DNA synthesis	[173]
CITE-seq	2017	Cellular indexing of transcriptomes and epitopes	[174]
REAP-seq	2017	The costimulatory effects of a CD27 agonist on human CD8⁺ lymphocytes	[175]
Apt-seq	2018	Differentiate distinct cell types	[176]
ECCITE-seq	2019	Clonotype-aware multimodal phenotyping of cancer samples	[177]
INs-seq	2020	Immunosuppressive role of Trem2 in cancer	[178]
SCITO-seq	2021	Cell surface protein abundance	[179]
inCITE-seq	2021	Identification of gene regulatory targets of nuclear proteins in tissues	[180]
Multi-Paired-seq	2022	Dynamic expression and correlations between mRNAs and proteins in individual cells	[181]

G&T-seq genome and transcriptome sequencing, DR-seq gDNA-mRNA sequencing, SIDR simultaneous isolation of genomic DNA and total RNA, DMF-DR-seq digital microfluidics gDNA-mRNA sequencing, scM&T-seq single-cell genome-wide methylome and transcriptome sequencing, scMT-seq single-cell methylome and transcriptome sequencing, scTrio-seq single-cell triple omics sequencing, sc-GEM single-cell analysis of genotype, expression and methylation, scNMT-seq single-cell nucleosome, methylation and transcription sequencing, snDrop-seq single-nucleus droplet-based sequencing, scTHS-seq single-cell transposome hypersensitive site sequencing, sciCAR single-cell combinatorial indexing of chromatin accessibility and mRNA, Paired-seq parallel analysis of individual cells for RNA expression and DNA accessibility by sequencing, SNARE-seq single-nucleus chromatin accessibility and mRNA expression sequencing, scCAT-seq single-cell chromatin accessibility and transcriptome sequencing, PLAYR proximity ligation assay for RNA, PEA/STA proximity extension assays/specific (RNA) target amplification, CITE-seq cellular indexing of transcriptomes and epitopes by sequencing, REAP-seq RNA expression and protein sequencing assay, Apt-seq aptamers and single cell sequencing, ECCITE-seq expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing, INs-seq intracellular staining and sequencing, SCITO-seq single-cell combinatorial indexed cytometry sequencing, inCITE-seq intranuclear cellular indexing of transcriptomes and epitopes, SNVs single nucleotide variants, DNA deoxyribonucleic acid, mRNA messenger RNA

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ISSN: 2054-9369

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