In situ sequencing for RNA analysis in preserved tissue and cells
Open accessAbstract
Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.
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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 [161]
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- Authors
- Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C., & Nilsson, M.
- Affiliations
- Stockholm University (SE)
- Uppsala University (SE)
- Broad Institute (US)
- Corresponding author
- Wählby, Carolina
- Nilsson, Mats
- Venue
- Nature Methods
- Published
- 2013-07-14
- Volume
- 10
- Issue
- 9
- Pages
- 857-860
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1972618510
- Cited by
- 934
- References
- 17
- Citations by year
- 2026: 69 · 2025: 122 · 2024: 146 · 2023: 104 · 2022: 92 · 2021: 86 · 2020: 67 · 2019: 45 · 2018: 55 · 2017: 41 · 2016: 42 · 2015: 25 · 2014: 33 · 2013: 5
- FWCI
- 15.69
- Type
- journal article
- Language
- en
- Open access
- green
- zenodo.org
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- in situ sequencing, RNA sequencing, single-cell gene expression profiling, point mutations, breast cancer
- MeSH terms
- Actins, Breast Neoplasms, Female, Humans, Proto-Oncogene Proteins, RNA, Messenger, Tissue Preservation, Proto-Oncogene Proteins p21(ras), Point Mutation, Sequence Analysis, RNA, ras Proteins, Receptor, ErbB-2, Erb-b2 Receptor Tyrosine Kinases, Gene Expression Profiling
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