Expansion Sequencing: Spatially PreciseIn SituTranscriptomics in Intact Biological Systems Article Swipe
Shahar Alon
,
Daniel Goodwin
,
Anubhav Sinha
,
Asmamaw T. Wassie
,
Fei Chen
,
Evan R Daugharthy
,
Yosuke Bando
,
Atsushi Kajita
,
Andrew G. Xue
,
Karl Marrett
,
Robert Prior
,
Yi Cui
,
Andrew C. Payne
,
Chun‐Chen Yao
,
Ho‐Jun Suk
,
Ru Wang
,
Chih-Chieh Yu
,
Paul W. Tillberg
,
Paul Reginato
,
Nikita Pak
,
Songlei Liu
,
Sukanya Punthambaker
,
Eswar Prasad R. Iyer
,
Richie E. Kohman
,
Jeremy A. Miller
,
Ed S. Lein
,
Ana Lako
,
Nicole Cullen
,
Scott J. Rodig
,
Karla Helvie
,
Daniel L. Abravanel
,
Nikhil Wagle
,
Bruce E. Johnson
,
Johanna Klughammer
,
Michal Slyper
,
Julia Waldman
,
Judit Jané‐Valbuena
,
Orit Rozenblatt–Rosen
,
Aviv Regev
,
George M. Church
,
Adam Marblestone
,
Edward S. Boyden
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.05.13.094268
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.05.13.094268
Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale. One Sentence Summary In situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.
Related Topics
Concepts
RNA
Computational biology
Biology
In situ
In situ hybridization
Transcriptome
DNA sequencing
Deep sequencing
Gene
Genome
Genetics
Gene expression
Chemistry
Organic chemistry
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2020.05.13.094268
- https://www.biorxiv.org/content/biorxiv/early/2020/05/15/2020.05.13.094268.full.pdf
- OA Status
- green
- Cited By
- 28
- References
- 132
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3025798397
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3025798397Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2020.05.13.094268Digital Object Identifier
- Title
-
Expansion Sequencing: Spatially PreciseIn SituTranscriptomics in Intact Biological SystemsWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-05-15Full publication date if available
- Authors
-
Shahar Alon, Daniel Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G. Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun‐Chen Yao, Ho‐Jun Suk, Ru Wang, Chih-Chieh Yu, Paul W. Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar Prasad R. Iyer, Richie E. Kohman, Jeremy A. Miller, Ed S. Lein, Ana Lako, Nicole Cullen, Scott J. Rodig, Karla Helvie, Daniel L. Abravanel, Nikhil Wagle, Bruce E. Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané‐Valbuena, Orit Rozenblatt–Rosen, Aviv Regev, George M. Church, Adam Marblestone, Edward S. BoydenList of authors in order
- Landing page
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https://doi.org/10.1101/2020.05.13.094268Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2020/05/15/2020.05.13.094268.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2020/05/15/2020.05.13.094268.full.pdfDirect OA link when available
- Concepts
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RNA, Computational biology, Biology, In situ, In situ hybridization, Transcriptome, DNA sequencing, Deep sequencing, Gene, Genome, Genetics, Gene expression, Chemistry, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
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28Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 2, 2023: 8, 2022: 6, 2021: 9Per-year citation counts (last 5 years)
- References (count)
-
132Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.revealing | 81 |
| abstract_inverted_index.specimens | 134 |
| abstract_inverted_index.thousands | 55 |
| abstract_inverted_index.biological | 32 |
| abstract_inverted_index.metastatic | 108 |
| abstract_inverted_index.nanoscale, | 141 |
| abstract_inverted_index.physically | 30, 132 |
| abstract_inverted_index.sequencing | 47, 130 |
| abstract_inverted_index.specimens, | 33 |
| abstract_inverted_index.throughout | 71 |
| abstract_inverted_index.untargeted | 36, 45 |
| abstract_inverted_index.microscopy, | 28 |
| abstract_inverted_index.multiplexed | 4, 116, 136 |
| abstract_inverted_index.resolution, | 11 |
| abstract_inverted_index.resolution. | 143 |
| abstract_inverted_index.sequencing. | 42 |
| abstract_inverted_index.subcellular | 23, 142 |
| abstract_inverted_index.transcripts | 19 |
| abstract_inverted_index.hippocampus, | 80 |
| abstract_inverted_index.organization | 96 |
| abstract_inverted_index.transcripts. | 63 |
| abstract_inverted_index.compartments. | 24 |
| abstract_inverted_index.layer-specific | 87 |
| abstract_inverted_index.position-dependent | 98 |
| abstract_inverted_index.nanoscale-resolution | 67 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5109593948 |
| countries_distinct_count | 4 |
| institutions_distinct_count | 42 |
| corresponding_institution_ids | https://openalex.org/I144112489, https://openalex.org/I4210104429, https://openalex.org/I4210109586, https://openalex.org/I4210142372 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.75 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.88492268 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |