Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Ribosome Profiling

Ribosome Profiling

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...

You might also read

Related Articles

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

Sort by

Same author

Bisphenol A induces a pro-angiogenic-like phenotype via the G protein-coupled receptor 30 (GPR30) pathway.

Scientific reports·2026

Same author

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.

Genome medicine·2026

Same author

Exploration of miR-326 delivery via biocompatible polymeric nanoparticles in medulloblastoma: A preliminary study.

Molecular therapy. Nucleic acids·2026

Same author

Circulating EV-microRNAs are dynamic biomarkers of resistance to therapeutic immunomodulation in metastatic melanoma.

Communications medicine·2026

Same author

The history and function of a circular RNA.

Nature communications·2026

Same author

Accelerating Leigh syndrome drug discovery through deep learning screening in brain organoids.

Nature communications·2026

Same journal

Computational protocol for modeling supported nanoparticle catalysts with strong metal-support interactions.

STAR protocols·2026

Same journal

Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN.

STAR protocols·2026

Same journal

A protocol for noninvasive quantification of dietary fat absorption in mice.

STAR protocols·2026

Same journal

Protocol for an AlCl<sub>3</sub>-induced Alzheimer's model in zebrafish larvae with optimized pH and behavioral assessment.

STAR protocols·2026

Same journal

Protocol for live cell barcoding and immunophenotyping of human hematological malignancies using cytometry by time of flight.

STAR protocols·2026

Same journal

Generating drug resistance models in human and murine cancer cell lines and assessing cross-resistance to chemotherapeutics and KRAS inhibitors.

STAR protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 4, 2025

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

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

Published on: July 6, 2022

Protocol for high-resolution 3D spatial transcriptomics using Open-ST.

Marie Schott¹, Daniel León-Periñán¹, Elena Splendiani²

¹Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany.

|December 21, 2024

Summary

This summary is machine-generated.

This study introduces Open-ST, a new protocol for high-resolution spatial transcriptomics (ST) in 2D and 3D tissue samples. Open-ST enables detailed molecular mapping for health and disease research.

Keywords:

RNA-seq bioinformatics cancer microscopy systems biology

More Related Videos

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

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

Published on: May 3, 2024

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Related Experiment Videos

Last Updated: Jun 4, 2025

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

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

Published on: July 6, 2022

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

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

Published on: May 3, 2024

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Spatial transcriptomics (ST) is crucial for dissecting molecular mechanisms in biological tissues.
Understanding spatial gene expression patterns is key to advancing research in health and disease.

Purpose of the Study:

To present an efficient and high-resolution protocol for 2D and 3D spatial transcriptomics.
To introduce Open-ST, a novel computational workflow for generating molecular maps of tissues.

Main Methods:

Repurposing Illumina flow cells into spatially barcoded capture areas.
Preparing spatial transcriptomics libraries from stained cryosections.
Detailed computational workflow for generating 2D/3D molecular maps aligned with histology.

Main Results:

Development of the Open-ST protocol for efficient and high-resolution spatial transcriptomics.
Creation of "virtual tissue blocks" that integrate molecular data with spatial information.
Demonstration of Open-ST's applicability to diverse tissue types, including clinical samples.

Conclusions:

Open-ST provides a robust method for high-resolution spatial transcriptomics in various tissue types.
The protocol facilitates the exploration of molecular pathways within their spatial context.
This approach enhances the understanding of molecular mechanisms in both health and disease.