Spatially resolved, highly multiplexed RNA profiling in single cells
Open accessAbstract
Multiplexed RNA imaging in single cells: The basis of cellular function is where and when proteins are expressed and in what quantities. Single-molecule fluorescence in situ hybridization (smFISH) experiments quantify the copy number and location of mRNA molecules; however, the numbers of RNA species that can be simultaneously measured by smFISH has been limited. Using combinatorial labeling with error-robust encoding schemes, Chen et al. simultaneously imaged 100 to 1000 RNA species in a single cell. Such large-scale detection allows regulatory interactions to be analyzed at the transcriptome scale. Science , this issue p. 10.1126/science.aaa6090
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Cellular identity and function are governed by elaborate regulatory circuits, many of which act through control of RNA expression.
“Cellular identity and function are governed by elaborate regulatory circuits, many of which act through control of RNA expression166,167.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [166]
merFISH and seqFISH use sequencing-by-hybridisation techniques for transcriptomic quantification.
“The recently developed methods of merFISH (Chen et al, 2015) and seqFISH (Shah et al, 2016b) use sequencing‐by‐hybridisation techniques for transcriptomic quantification.”
From Using single-cell genomics to understand developmental processes and cell fate decisions (2018) · cites this paper as Chen et al, 2015
MERFISH increased the number of RNA molecules simultaneously imaged in single cells using combinatorial labelling and sequential imaging.
“A year later, MERFISH substantially increased the number of RNA molecules that could be simultaneously imaged in single cells by utilizing combinatorial labelling and sequential imaging of multiple readout hybridizations101.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [101]
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- Authors
- Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Chen, Kok Hao
- Boettiger, Alistair N.
- Moffitt, Jeffrey R.
- Zhuang, Xiaowei
- Venue
- Science
- Published
- 2015-04-24
- Volume
- 348
- Issue
- 6233
- Pages
- aaa6090-aaa6090
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4662681
- OpenAlex
- W2042789810
- Cited by
- 2,969
- References
- 53
- Citations by year
- 2026: 478 · 2025: 491 · 2024: 466 · 2023: 314 · 2022: 259 · 2021: 261 · 2020: 210 · 2019: 161 · 2018: 128 · 2017: 95 · 2016: 69 · 2015: 33 · 2014: 2 · 2012: 1
- FWCI
- 47.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- Howard Hughes Medical Institute
- Damon Runyon Foundation
- Helen Hay Whitney Foundation
- Agency for Science, Technology and Research of Singapore
- Jane Coffins Child Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Keywords
- MERFISH, spatial transcriptomics, gene regulatory networks, single-molecule imaging
- MeSH terms
- Fibroblasts, Humans, RNA, Messenger, RNA Probes, In Situ Hybridization, Fluorescence, Gene Expression Profiling, Molecular Imaging, High-Throughput Screening Assays, Single-Cell Analysis, Transcriptome
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