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Related Experiment Video

Updated: Dec 12, 2025

Imaging Intermediate Filaments and Microtubules with 2-dimensional Direct Stochastic Optical Reconstruction Microscopy
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Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue.

Jianquan Xu1, Hongqiang Ma1, Yang Liu1

  • 1Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania.

Current Protocols in Cytometry
|August 8, 2020
PubMed
Summary

PathSTORM enables high-resolution imaging of chromatin structure in pathology tissues. This optimized protocol visualizes higher-order chromatin organization in formalin-fixed, paraffin-embedded samples for disease research.

Keywords:
higher-order chromatin structurepathological tissuestochastic optical reconstruction microscopy (STORM)super-resolution fluorescence microscopy

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Area of Science:

  • Cell Biology
  • Microscopy
  • Genomics

Background:

  • Direct visualization of higher-order chromatin structure is crucial for understanding gene expression.
  • Pathological processes involve chromatin structure changes, necessitating analysis in clinical samples.
  • Formalin-fixed, paraffin-embedded (FFPE) tissues are the standard for pathological sample preservation.

Purpose of the Study:

  • To detail an optimized stochastic optical reconstruction microscopy (STORM) protocol, named PathSTORM.
  • To enable high-quality super-resolution imaging of higher-order chromatin organization in pathological tissues.
  • To provide methods for fluorescence staining and key technical factors for STORM imaging in FFPE samples.

Main Methods:

  • Development of PathSTORM, an optimized STORM protocol.
  • Detailed methods for fluorescence staining of DNA and histone proteins.
  • Key technical considerations for STORM imaging in pathological tissue samples.

Main Results:

  • Successful application of PathSTORM for super-resolution imaging of chromatin in FFPE tissues.
  • High-quality visualization of densely packed higher-order chromatin organization.
  • Demonstration of essential steps for fluorescence staining and STORM data processing.

Conclusions:

  • PathSTORM is an effective protocol for visualizing chromatin structure in pathological FFPE tissues.
  • The protocol facilitates research into the role of chromatin organization in disease.
  • This method advances the study of molecular-scale chromatin organization in clinical samples.