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Related Experiment Video

Updated: Mar 1, 2026

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry
06:51

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry

Published on: November 14, 2025

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Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection.

Haibiao Gong1, Xiaohui Wang2, Benjamin Liu2

  • 1Fluidigm Corporation, South San Francisco, CA, 94080, USA. haibiao.gong@fluidigm.com.

Scientific Reports
|June 7, 2017
PubMed
Summary

This study reveals how protein and mRNA levels correlate in single cells using a novel dual-analyte detection method. This integrated approach offers deeper biological insights than traditional bulk analysis.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Proteomics

Background:

  • Understanding the relationship between protein and mRNA levels is crucial for deciphering gene expression regulation.
  • Single-cell analysis provides higher resolution for studying cellular heterogeneity compared to bulk methods.

Purpose of the Study:

  • To develop and validate an integrated workflow for simultaneous detection of proteins and mRNAs in single cells.
  • To investigate the correlation patterns between protein and mRNA expression within individual cells.
  • To explore the utility of single-cell protein-mRNA profiling for identifying distinct cellular subpopulations.

Main Methods:

  • An integrated workflow combining oligo extension reaction (OER) for protein-to-DNA conversion and reverse transcription for mRNA detection.
  • Unsupervised gene expression profiling, including principal component analysis and hierarchical clustering.
  • Violin plot analysis to compare protein and mRNA distribution patterns.
  • Correlation coefficient analysis to characterize protein-mRNA relationships in different subpopulations.

Main Results:

  • Demonstrated successful co-detection of proteins and mRNAs in single cells.
  • Identified genes with similar distribution patterns for both protein and mRNA levels.
  • Showcased the ability to separate cells into subpopulations based on integrated protein-mRNA expression profiles.
  • Revealed distinct correlation coefficient values among different cellular subpopulations.

Conclusions:

  • The integrated workflow enables comprehensive analysis of protein-mRNA correlations at the single-cell level.
  • Single-cell protein-mRNA profiling can uncover cellular heterogeneity and distinct biological states.
  • This approach offers insights unattainable through traditional bulk analysis methods.