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

DNA Microarrays02:34

DNA Microarrays

17.3K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
17.3K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
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...
3.5K

You might also read

Related Articles

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

Sort by
Same author

Comment on "Diagnostic Guidance for Chronic Complex Regional Pain Syndrome Type I and Type II from The American Society of Interventional Physicians (ASIPP)".

Pain physician·2026
Same author

Clinical practices in general anaesthesia for caesarean section: A nationwide cross-sectional survey.

European journal of anaesthesiology and intensive care·2026
Same author

Sex-specific molecular and cellular phenotypes during resolution of neuropathic pain in dorsal root ganglia.

Cell reports·2026
Same author

Defining "regional" pain.

Pain·2026
Same author

Relief and blunted defensive conditioned responses in girls with non-suicidal self-injury behaviors.

European child & adolescent psychiatry·2026
Same author

Cytokine Dynamics in Bortezomib-Induced Peripheral Neuropathy: Challenges in Translating Preclinical Findings to Humans.

Journal of the peripheral nervous system : JPNS·2026
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jun 25, 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

4.9K

Comparative Methods for Demystifying Spatial Transcriptomics.

Michael Sammeth1,2, Susann Mudra3, Sina Bialdiga3

  • 1Coburg University of Applied Sciences and Art, Department of Applied Sciences and Health, Coburg, Germany. micha@sammeth.net.

Methods in Molecular Biology (Clifton, N.J.)
|May 31, 2024
PubMed
Summary
This summary is machine-generated.

Spatial Transcriptomics (ST) analysis, particularly with 10x Visium, involves gene expression profiling on tissue sections. This study evaluates how spot selection and reference genomes impact ST data analysis results.

Keywords:
10x Visium platformDifferential gene expressionGene expression clusteringRNA-SeqSpatial transcriptomics

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

2.7K
Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level
09:45

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Published on: March 14, 2022

2.9K

Related Experiment Videos

Last Updated: Jun 25, 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

4.9K
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

2.7K
Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level
09:45

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Published on: March 14, 2022

2.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Spatial Transcriptomics (ST) enables parallel RNA sequencing on tissue sections, crucial for experiments like neuronal assays where single-cell sequencing falters.
  • ST platforms, such as 10x Visium, capture thousands of RNA readouts from micrometer-scale spots on tissue sections, presenting unique analytical challenges.

Purpose of the Study:

  • To analyze the gene expression morphology of spots in ST experiments to delineate cell mixtures and identify marker genes.
  • To investigate the impact of spot selection and the choice of genome/transcriptome references on ST analysis results using the Visium platform's software suite.

Main Methods:

  • The study breaks down the ST analysis pipeline into four steps: image analysis, read alignment, gene quantification, and spot clustering.
  • Comparative analyses were performed using reads from different spot subsets and alternative genome/transcriptome references.

Main Results:

  • The choice of genome and transcriptome references significantly influences ST analysis outcomes.
  • Spot selection critically impacts the results obtained from the manufacturer's ST analysis pipeline.

Conclusions:

  • Understanding the influence of spot selection and reference choice is vital for accurate interpretation of Spatial Transcriptomics data.
  • The findings highlight the importance of optimizing these parameters within the Visium ST analysis pipeline for reliable biological insights.