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Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
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Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
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Metadata
- Authors
- Longo, S. K., Guo, M. G., Ji, A. L., & Khavari, P. A.
- Affiliations
- Stanford Cancer Institute (US)
- VA Palo Alto Health Care System (US)
- Corresponding author
- Khavari, Paul A.
- Venue
- Nature Reviews Genetics
- Published
- 2021-06-18
- Volume
- 22
- Issue
- 10
- Pages
- 627-644
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC9888017
- OpenAlex
- W3171692328
- Cited by
- 1,059
- References
- 183
- Citations by year
- 2026: 233 · 2025: 203 · 2024: 242 · 2023: 196 · 2022: 157 · 2021: 27
- FWCI
- 16.92
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (R01CA142635)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR049737, R01AR043799, R01AR076965)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- single-cell RNA sequencing, spatial transcriptomics, data integration, intercellular communication, tissue dynamics, in situ sequencing, cell localization
- MeSH terms
- Animals, Cell Communication, Humans, Software, Sequence Analysis, RNA, Computational Biology, Single-Cell Analysis, Transcriptome
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