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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: May 15, 2026

Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells
09:18

Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells

Published on: September 7, 2018

RNA-based CLEM (RCLEM) bridging RNA localisation and ultrastructural mapping in 3D.

Daan Verhaege1,2, Lore Van Acker1,2, Camille Wagner1,2

  • 1VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium.

Journal of Microscopy
|May 14, 2026
PubMed
Summary

We developed a 3D RNA-based correlated light and electron microscopy (RCLEM) workflow to visualize mRNA within its ultrastructural context. This advanced spatial transcriptomics method overcomes light microscopy limitations for high-resolution tissue analysis.

Keywords:
CLEM workflowRCLEMSBF‐SEMhigh‐resolution confocal imaging

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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Published on: August 6, 2014

Related Experiment Videos

Last Updated: May 15, 2026

Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells
09:18

Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells

Published on: September 7, 2018

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
12:20

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Published on: August 6, 2014

Area of Science:

  • Molecular Biology
  • Cell Biology
  • Microscopy

Background:

  • Spatial transcriptomics methods like single-cell RNA sequencing (scRNA-seq) map gene expression in tissues.
  • Current spatial transcriptomics rely on light microscopy (LM), which has resolution limits for subcellular details.
  • Existing correlative imaging methods struggle with RNA detection resolution due to LM optical constraints.

Purpose of the Study:

  • To develop a high-resolution 3D workflow for visualizing RNA localization within the ultrastructural context of intact tissues.
  • To overcome the resolution limitations of current light microscopy-based spatial transcriptomics techniques.
  • To enable precise correlation between mRNA expression and cellular ultrastructure for advanced biological insights.

Main Methods:

  • Developed a 3D RNA-based correlated light and electron microscopy (RCLEM) workflow.
  • Integrated RNA labeling with serial block-face scanning electron microscopy (SBF-SEM).
  • Optimized detergent conditions for probe accessibility in thick, whole-mount tissues while preserving ultrastructure.

Main Results:

  • Achieved high-resolution 3D visualization of RNA molecules within their native ultrastructural environment.
  • Demonstrated precise 3D correlation between mRNA expression and electron microscopy features in choroid plexus and liver tissues.
  • Enabled detailed morphological characterization of rare cell subtypes defined by scRNA-seq.

Conclusions:

  • The RCLEM workflow provides a powerful platform for integrative, high-resolution spatial transcriptomic analysis.
  • This antibody-independent method bridges gene expression data with precise cellular morphology.
  • The protocol is broadly applicable to diverse complex tissues for advanced spatial analyses.