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

17.4K
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...
17.4K
Regulated mRNA Transport02:22

Regulated mRNA Transport

6.3K
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
6.3K
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

Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids.

Nature communications·2026
Same author

Interpretable deep generative ensemble learning for single-cell omics with Hydra.

Molecular systems biology·2026
Same author

Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy-Naïve Localized Prostate Cancer.

Cancer research·2026
Same author

Phosphoproteomics of aged insulin-resistant bone identifies P70S6K phosphorylation of AFF4 as a gene-specific transcriptional regulator.

Nature communications·2025
Same author

Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma.

Nature communications·2025
Same author

Connecting cilium, stress response, and proteostasis abnormalities inform variant and therapy assessment in RPGRIP1 retinal organoids.

Stem cell reports·2025
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: Jul 5, 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

Evaluating spatially variable gene detection methods for spatial transcriptomics data.

Carissa Chen1, Hani Jieun Kim2, Pengyi Yang3,4,5

  • 1Computational Systems Biology Group, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia.

Genome Biology
|January 15, 2024
PubMed
Summary
This summary is machine-generated.

This study benchmarks methods for identifying spatially variable genes (SVGs) in spatial transcriptomics. It reveals significant discrepancies between methods, impacting downstream analysis and highlighting the need for careful selection.

More Related Videos

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

3.0K
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

2.8K

Related Experiment Videos

Last Updated: Jul 5, 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
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

3.0K
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

2.8K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying genes that vary spatially within tissues is crucial for spatial transcriptomics.
  • Numerous methods for detecting spatially variable genes (SVGs) exist, but a lack of benchmarking hinders method selection.

Purpose of the Study:

  • To systematically evaluate popular SVG detection methods across diverse spatial transcriptomics datasets.
  • To assess method concordance, statistical significance reliability, accuracy, robustness, and downstream performance.
  • To consider practical aspects like computational efficiency for SVG identification.

Main Methods:

  • Comprehensive benchmarking of multiple SVG detection algorithms.
  • Analysis across various tissue types, biotechnologies, and spatial resolutions.
  • Evaluation of statistical significance, accuracy, robustness, and downstream application performance.

Main Results:

  • Significant discrepancies were observed among different SVG detection methods.
  • Method performance varied across diverse spatial transcriptomics datasets.
  • The reliability of statistical significance reporting differed notably between methods.

Conclusions:

  • The study highlights critical differences in SVG identification across methods, impacting data interpretation.
  • Provides guidance for selecting appropriate SVG detection tools for spatial transcriptomics.
  • Serves as a foundational reference for future development of SVG identification methods.