Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Mutant IDH1 blocks neutropoiesis by repressing myeloid progenitor programs.

Blood·2026
Same author

Switching Tracks: Activity of Entrectinib After Progression While on Larotrectinib in Neurotrophin Receptor Tyrosine Kinase-Fused Pediatric High-Grade CNS Tumors.

JCO precision oncology·2026
Same author

Author Correction: Multidimensional profiling of heterogeneity in supratentorial ependymomas.

Nature·2026
Same author

Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes.

Cancer cell·2026
Same author

Ependymoma group-specific blood-brain barrier differences uncovered by a multi-omics approach.

Scientific reports·2026
Same author

Developmental determinants of male bias in medulloblastoma.

bioRxiv : the preprint server for biology·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
Same journal

Mapping the landscape of allele-specific expression in porcine genomes.

Genome biology·2026
Same journal

Genomic sequence evolution underlying human neocortical interareal diversification.

Genome biology·2026
Same journal

Regulatory mechanisms driven by functional 3'-UTR variants in alcohol use disorder and related traits.

Genome biology·2026
Same journal

A longitudinal single-nucleus transcriptomic atlas of bovine placentation reveals dynamic cellular hierarchies and regulatory programs.

Genome biology·2026
See all related articles

Related Experiment Video

Updated: Sep 18, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

5.0K

Comparison of spatial transcriptomics technologies using tumor cryosections.

Anne Rademacher1,2, Alik Huseynov3, Michele Bortolomeazzi3

  • 1Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Genome Biology
|June 20, 2025
PubMed
Summary
This summary is machine-generated.

Comparing spatial transcriptomics technologies reveals imaging-based methods excel at mapping tumor microenvironments. This study provides a framework for selecting the best spatial transcriptomics tools for solid tumor research.

Keywords:
MERFISHMedulloblastomaMerscopeMolecular CartographyRNAscopeSpatial transcriptomicsVisiumXenium

More Related Videos

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.3K
Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses
08:17

Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses

Published on: December 12, 2016

16.0K

Related Experiment Videos

Last Updated: Sep 18, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

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

Published on: July 6, 2022

5.0K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.3K
Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses
08:17

Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses

Published on: December 12, 2016

16.0K

Area of Science:

  • Molecular biology
  • Genomics
  • Cancer research

Background:

  • Spatial transcriptomics offers insights into tumor heterogeneity and microenvironment.
  • Selecting the right spatial transcriptomics technology is challenging due to rapid method development.
  • This study compares imaging-based (RNAscope HiPlex, Molecular Cartography, Merscope, Xenium) and sequencing-based (Visium) methods.

Purpose of the Study:

  • To compare the performance of different spatial transcriptomics technologies.
  • To guide researchers in selecting appropriate methods for their objectives.
  • To evaluate spatial transcriptomics for studying medulloblastoma with extensive nodularity (MBEN).

Main Methods:

  • Comparative analysis of four imaging-based and one sequencing-based spatial transcriptomics technology.
  • Application to cryosections of medulloblastoma with extensive nodularity (MBEN).
  • Development of approaches to assess method sensitivity, specificity, and unique attributes.

Main Results:

  • Automated imaging-based spatial transcriptomics effectively delineates MBEN microanatomy and captures cell-type-specific transcriptomes.
  • Sensitivity, specificity, and unique attributes of each method were compared to aid in selection.
  • Reimaging slides post-analysis enhances cell segmentation and integrates additional transcript and protein data.

Conclusions:

  • Significant distinctions exist between spatial transcriptomics technologies.
  • A framework is provided for evaluating and selecting spatial transcriptomics methods.
  • Strategies to improve resolution and scope advance spatial transcriptomics applications in solid tumor research.