Cited by 951Single-cell and spatial transcriptomicsMolecular Biology Techniques and ApplicationsGenomics and Phylogenetic Studies

In situ sequencing for RNA analysis in preserved tissue and cells

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Ke, Rongqin, Mignardi, Marco, Pacureanu, Alexandra, Svedlund, Jessica, Botling, Johan, Wählby, Carolina, Nilsson, Mats·2013·Nature Methods

Abstract

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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Crossref · 10.1038/nmeth.2563

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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.”

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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
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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