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Related Experiment Video

Updated: Apr 15, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

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

Kok Hao Chen¹, Alistair N Boettiger¹, Jeffrey R Moffitt¹

¹Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Science (New York, N.Y.)

|April 11, 2015

Summary

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) enables precise RNA quantification and spatial mapping in single cells. This technique reveals gene regulatory networks and unannotated gene functions through comprehensive transcriptome analysis.

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Last Updated: Apr 15, 2026

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Published on: July 6, 2022

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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

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Published on: December 2, 2009

Area of Science:

Molecular Biology
Genomics
Cell Biology

Background:

Understanding cellular behavior requires knowledge of gene expression and spatial transcriptome.
Single-cell analysis is crucial for deciphering cellular complexity.

Purpose of the Study:

To develop a single-molecule imaging approach for quantifying and localizing thousands of RNA species in single cells.
To leverage this technology for gene regulatory network inference and functional gene discovery.

Main Methods:

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) was employed.
Error-robust encoding schemes were utilized to overcome labeling and detection errors.
Imaging of 100-1000 distinct RNA species in hundreds of single cells was achieved.

Main Results:

Accurate copy numbers and spatial localizations of thousands of RNA species were determined.
Correlation analysis of gene pairs revealed insights into gene regulatory networks.
Novel functions for unannotated genes were predicted.
Distinct RNA spatial patterns correlating with protein properties were identified.

Conclusions:

MERFISH provides a powerful tool for high-resolution spatial transcriptomics.
The method facilitates the discovery of gene functions and regulatory relationships.
Spatial RNA distribution patterns offer insights into cellular mechanisms.