Highly Multiplexed Subcellular RNA Sequencing in Situ
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Transcripts Visualized in Situ: Despite advances, current methods for single-cell sequencing are unable to resolve transcript location within the cell, so Lee et al. (p. 1360 , published online 27 February) developed a method of fluorescent in situ RNA sequencing (FISSEQ) that works in vivo to show messenger RNA localization within cells. The method amplifies complementary DNA targets by rolling circle amplification, and then in situ cross-linking locks amplicons to produce ample, highly localized templates for three-dimensional sequencing. The technique was tested in fibroblasts to reveal the differences between individual cells during wound repair.
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A different hurdle to successful application of reference-based mapping occurs in normal tissues such as the retina, in which functionally similar cells are mosaically organized.
“A different hurdle to successful application of such approaches occurs in normal tissues, such as the retina161,162, in which functionally similar cells are in fact mosaically organized.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [162]
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- Authors
- Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., Peters, D. T., Turczyk, B. M., Marblestone, A. H., Inverso, S. A., Bernard, A., Mali, P., Rios, X., Aach, J., & Church, G. M.
- Affiliations
- Harvard University (US)
- Allen Institute for Brain Science (US)
- Corresponding author
- Lee, Je Hyuk
- Daugharthy, Evan R.
- Church, George M.
- ORCID
- Venue
- Science
- Published
- 2014-03-21
- Volume
- 343
- Issue
- 6177
- Pages
- 1360-1363
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4140943
- OpenAlex
- W2151013106
- Cited by
- 973
- References
- 19
- Citations by year
- 2026: 57 · 2025: 57 · 2024: 77 · 2023: 75 · 2022: 86 · 2021: 95 · 2020: 91 · 2019: 88 · 2018: 84 · 2017: 84 · 2016: 79 · 2015: 56 · 2014: 39 · 2013: 2
- FWCI
- 35.24
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (RC2HL102815)
- National Institute of Mental Health (MH098977, U01MH098977)
- National Human Genome Research Institute (P50HG005550)
- National Institute of General Medical Sciences (T32GM007753, T32GM080177, GM080177)
- 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 › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- subcellular RNA localization, spatial gene expression, DNA barcoding, wound healing, human fibroblasts, tissue sections, single-molecule detection, gene expression regulation
- MeSH terms
- Base Sequence, Cell Line, Cells, Cultured, Fluorescence, Humans, RNA, Messenger, Wound Healing, Sequence Analysis, RNA, DNA, Complementary, Gene Expression Profiling, Transcription Initiation Site, Induced Pluripotent Stem Cells, Single-Cell Analysis, Transcriptome
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