Evidence map›Paper›PMID 33509999›Full record

ArticleScience (New York, N.Y.)2021

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett and 33 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 272 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
272citing papers in PubMed, 3 pooled it
23.6field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

272 citing papers in PubMed, 3 syntheses or guidelines pooled it, 398 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Pooled it
  4. Review
  5. Review
  6. Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026
    Review
  7. Review
  8. Article
  9. Article
  10. Review
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Thousandfold Expansion Microscopy.bioRxiv : the preprint server for biology · 2026
    Article
  18. Transcriptomics Insights into Spinal Cord Injury for Therapy Development.International journal of molecular sciences · 2026
    Review
  19. Global deletion ofbioRxiv : the preprint server for biology · 2026
    Article
  20. Review

212 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

43 authors at 9 institutions in 2 countries.

Shahar Alon *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-7458-3478
Daniel R Goodwin *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-1311-5232
Anubhav Sinha *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-1545-3163
Asmamaw T Wassie *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Fei Chen *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Evan R DaugharthyDepartment of Genetics, Harvard Medical School, Boston, MA, USA.ORCID https://orcid.org/0000-0002-5782-0056
Yosuke BandoDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-9150-6503
Atsushi KajitaFixstars Solutions Inc, Irvine, CA, USA.
Andrew G XueDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-8575-8376
Karl MarrettFixstars Solutions Inc, Irvine, CA, USA.
Robert PriorFixstars Solutions Inc, Irvine, CA, USA.ORCID https://orcid.org/0000-0002-4428-3212
Yi CuiDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-8597-0174
Andrew C PayneDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-7212-6994
Chun-Chen YaoDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Ho-Jun SukDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Ru WangDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Chih-Chieh Jay YuDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0001-8713-0446
Paul TillbergDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-2568-2365
Paul ReginatoDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-7525-9047
Nikita PakDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-7288-0479
Songlei LiuDepartment of Genetics, Harvard Medical School, Boston, MA, USA.ORCID https://orcid.org/0000-0001-8607-8260
Sukanya PunthambakerDepartment of Genetics, Harvard Medical School, Boston, MA, USA.ORCID https://orcid.org/0000-0001-6878-9990
Eswar P R IyerWyss Institute for Biologically Inspired Engineering, Boston, MA, USA.ORCID https://orcid.org/0000-0001-9395-5890
Richie E KohmanDepartment of Genetics, Harvard Medical School, Boston, MA, USA.ORCID https://orcid.org/0000-0002-7412-671X
Jeremy A MillerAllen Institute for Brain Science, Seattle, WA, USA.ORCID https://orcid.org/0000-0003-4549-588X
Ed S LeinAllen Institute for Brain Science, Seattle, WA, USA.ORCID https://orcid.org/0000-0001-9012-6552
Ana LakoCenter for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA.ORCID https://orcid.org/0000-0003-2931-6212
Nicole CullenCenter for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA.
Scott RodigCenter for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA.
Karla HelvieCenter for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA.
Daniel L AbravanelBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-0129-1618
Nikhil WagleCenter for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID https://orcid.org/0000-0003-3332-9438
Bruce E JohnsonCenter for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA.
Johanna KlughammerBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-3628-9278
Michal SlyperBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-3002-0366
Julia WaldmanBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-0584-5833
Judit Jané-ValbuenaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-5651-1745
Orit Rozenblatt-RosenBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0001-6313-3570
Aviv RegevBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID https://orcid.org/0000-0003-3293-3158
IMAXT Consortium
George M Church *Department of Genetics, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu edboyden@mit.edu.ORCID https://orcid.org/0000-0002-0775-2913
Adam H Marblestone *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Edward S Boyden *Department of Media Arts and Sciences, MIT, Cambridge, MA, USA. gchurch@genetics.med.harvard.edu edboyden@mit.edu.ORCID https://orcid.org/0000-0002-0419-3351
Broad Institute · USHoward Hughes Medical Institute · USEngineering Arts (United States) · USMcGovern Institute for Brain Research · USHarvard University · USDana-Farber Cancer Institute · USBar-Ilan University · ILFixstars Solutions (United States) · USAllen Institute for Brain Science · US

Funding

Tool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI ARLOTTA, PAOLA, HUANG, Z JOSH · 2017 to 2021
$64.5M
Causal Transcriptional Consequences of Human Genetic VariationP50HG005550 · NHGRI · HARVARD MEDICAL SCHOOL · PI CHURCH, GEORGE M · 2010 to 2014
$19.0M
Physician Scientist Training in Cancer ResearchT32CA009172 · NCI · DANA-FARBER CANCER INSTITUTE · PI Jennifer R Brown, James A. DeCaprio · 1985 to 2026
$17.1M
Center for Genomically Engineered OrgansRM1HG008525 · NHGRI · HARVARD MEDICAL SCHOOL · PI CHURCH, GEORGE M · 2015 to 2019
$10.2M
Recording neural activities onto DNAR01MH103910 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI BOYDEN, EDWARD S., CHURCH, GEORGE M · 2013 to 2017
$9.5M
Expansion MicroscopyR01EB024261 · NIBIB · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S. · 2017 to 2025
$4.6M
Neuroimaging Training ProgramT32EB001680 · NIBIB · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BRUCE R ROSEN · 2003 to 2026
$3.8M
High-Performance Imaging Through Scattering Living TissueR01DA045549 · NIDA · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S. · 2017 to 2020
$3.5M
RNA Scaffolds for Cell Specific Multiplexed Neural ObservationR01MH114031 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S. · 2017 to 2020
$2.8M
An Accessible Optical Toolbox for Saturated Nanoscale Analysis of Neural ArchitectureR01MH110932 · NIMH · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOYDEN, EDWARD S., CAI, DAWEN · 2016 to 2019
$2.8M
Scalable Cell- and Circuit-Targeted ElectrophysiologyR01NS102727 · NINDS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S., FOREST, CRAIG · 2017 to 2020
$2.2M
Whole-brain recording into nucleic acids using template-independent polymerasesUF1NS107697 · NINDS · NORTHWESTERN UNIVERSITY · PI TYO, KEITH EDWARD JAGGARD · 2018 to 2018
$1.7M
Cancer Research UK 20544Cancer Research UK 21143NCI NIH HHS HHSN261201500003CNCI NIH HHS HHSN261201500003INCI NIH HHS T32 CA009172NHGRI NIH HHS P50 HG005550NHGRI NIH HHS RM1 HG008525NIBIB NIH HHS R01 EB024261NIBIB NIH HHS T32 EB001680NIDA NIH HHS R01 DA045549NIH HHS S10 OD021692NIMH NIH HHS R01 MH103910NIMH NIH HHS R01 MH110932NIMH NIH HHS R01 MH114031NIMH NIH HHS U19 MH114821NINDS NIH HHS R01 NS102727NINDS NIH HHS UF1 NS107697
6 · The paper itself

Abstract

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 the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the 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.

Indexed as

AnimalsBreast NeoplasmsDendritic SpinesFemaleGene Expression ProfilingHumansMiceMolecular ImagingSequence Analysis, RNASingle-Cell AnalysisVisual Cortex

Identifiers

PMID33509999
PMCPMC7900882
OpenAlexW3125011419

What OpenQuestion holds

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LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.