The expanding vistas of spatial transcriptomics
Open accessAbstract
The formation and maintenance of tissue integrity requires complex, coordinated activities by thousands of genes and their encoded products. Until recently, transcript levels could only be quantified for a few genes in tissues, but advances in DNA sequencing, oligonucleotide synthesis and fluorescence microscopy have enabled the invention of a suite of spatial transcriptomics technologies capable of measuring the expression of many, or all, genes in situ. These technologies have evolved rapidly in sensitivity, multiplexing and throughput. As such, they have enabled the determination of the cell-type architecture of tissues, the querying of cell-cell interactions and the monitoring of molecular interactions between tissue components. The rapidly evolving spatial genomics landscape will enable generalized high-throughput genomic measurements and perturbations to be performed in the context of tissues. These advances will empower hypothesis generation and biological discovery and bridge the worlds of tissue biology and genomics.
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There is increasing interest in spatial techniques, including single-cell resolution spatial transcriptomics, epigenomics and proteomics.
“Moreover, there is increasing interest in spatial techniques, including single-cell resolution spatial transcriptomics, epigenomics and proteomics57.”
From scPerturb: harmonized single-cell perturbation data (2024) · cites this paper as [57]
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Flagged first, then by citations
Research works printed but not linked: 1
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- Authors
- Tian, L., Chen, F., & Macosko, E. Z.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Chen, Fei
- Macosko, Evan Z.
- Venue
- Nature Biotechnology
- Published
- 2022-10-03
- Volume
- 41
- Issue
- 6
- Pages
- 773-782
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC10091579
- OpenAlex
- W4300862018
- Cited by
- 539
- References
- 90
- Citations by year
- 2026: 133 · 2025: 193 · 2024: 149 · 2023: 60 · 2022: 4
- FWCI
- 10.91
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | National Institutes of Health (UH3CA246632, R01HG010647)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Keywords
- spatial transcriptomics, spatial genomics, in situ gene expression, cell-cell interactions, tissue integrity, multiplexing, tissue biology
- MeSH terms
- Sequence Analysis, DNA, Gene Expression Profiling, Genomics, Transcriptome
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