Evidence map›Paper›PMID 25858977›Full record

ArticleScience (New York, N.Y.)2015

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,739 papers.

0numbers the graph read from it
0cells of the map it votes in
1,739citing papers in PubMed
–field-weighted citation impact
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

1,739 citing papers in PubMed.

  1. Review
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  12. 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
  13. Pervasive Somatic Mutations inbioRxiv : the preprint server for biology · 2026
    Article
  14. Article
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  17. Article
  18. Article
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  20. Biochemistry and biophysics reports · 2026
    Article

1,679 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Kok Hao ChenHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Alistair N BoettigerHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Jeffrey R MoffittHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Siyuan WangHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Xiaowei ZhuangHoward Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. Department of Physics, Harvard University, Cambridge, MA 02138, USA. zhuang@chemistry.harvard.edu.

Funding

Dynamic cellular architecture of bacteria by system-wide super-resolution imagingR01GM096450 · NIGMS · HARVARD UNIVERSITY · PI XIE, XIAOLIANG SUNNEY, ZHUANG, XIAOWEI · 2010 to 2014
$3.7M
Single-molecule studies of ATP-dependent chromatin remodelingR01GM105637 · NIGMS · HARVARD UNIVERSITY · PI ZHUANG, XIAOWEI · 2013 to 2016
$1.3M
Howard Hughes Medical InstituteNIGMS NIH HHS R01 GM096450NIGMS NIH HHS R01 GM105637
6 · The paper itself

Abstract

Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here, we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 to 1000 distinct RNA species in hundreds of individual cells. Correlation analysis of the ~10(4) to 10(6) pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.

Indexed as

TranscriptomeFibroblastsGene Expression ProfilingHigh-Throughput Screening AssaysHumansIn Situ Hybridization, FluorescenceMolecular ImagingRNA, MessengerRNA ProbesSingle-Cell AnalysisRNA, MessengerRNA Probes

Identifiers

PMID25858977
PMCPMC4662681

What OpenQuestion holds

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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.