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Related Concept Videos

Penis01:29

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The penis serves a dual role in sexual reproduction and urination. It consists of three main regions: the glans penis, the body, and the root, each with distinct functions and unique anatomical features.
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The glans penis, or the head, is the terminal part of the penis and houses the external urethral orifice, the exit point for urine and semen. Covered by the prepuce, or foreskin, the glans is noted for its sensitivity and plays a key role in sexual pleasure. The body of the...
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Men's health issues are increasingly recognized as significant, with several conditions posing common threats. Among these, testicular cancer is especially prevalent in younger men, particularly those aged 20 to 35 years. The disease often manifests as a painless mass in the testicles, sometimes accompanied by a sensation of heaviness or a dull ache.
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Related Experiment Video

Updated: May 4, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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VisualZoneR: A computational protocol to identify compartmental zones from single-cell spatial transcriptomics using

Thomas Kerzel1, Stefano Beretta1, Luigi Naldini2

  • 1San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.

STAR Protocols
|July 27, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces VisualZoneR, an R-based method for analyzing spatial transcriptomics data. It identifies distinct tissue zones and measures transcriptomic changes, aiding in understanding complex biological environments.

Keywords:
BioinformaticsCancerGene ExpressionSingle Cell

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Spatial transcriptomics technologies like Visium and Visium HD generate complex datasets.
  • Analyzing compartmental zones within tissues is crucial for understanding biological processes.
  • Existing methods may not fully capture the nuances of spatial transcriptomic data.

Purpose of the Study:

  • To present a protocol for identifying compartmental zones in single-cell spatial transcriptomics data.
  • To demonstrate the application of VisualZoneR for analyzing tissue heterogeneity.
  • To enable the measurement of transcriptomic changes within identified zones.

Main Methods:

  • Utilizing VisualZoneR, an R-based technique.
  • Processing spatial transcriptomics data from Visium or Visium HD.
  • Identifying distinct tissue zones (e.g., healthy liver, metastatic areas).
  • Integrating multiple samples and grouping transcriptomic spots based on proximity to boundaries.

Main Results:

  • Successful identification of distinct compartmental zones within tissue samples.
  • Quantification of transcriptomic alterations across different zones.
  • Demonstration of VisualZoneR's capability to analyze spatial relationships and tissue microenvironments.

Conclusions:

  • VisualZoneR provides a robust framework for analyzing spatial transcriptomics data.
  • The protocol facilitates the identification of tissue compartments and associated gene expression patterns.
  • This method enhances the understanding of spatial heterogeneity in biological tissues.