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

RNA-seq03:21

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 microarray-based...
Ribosome Profiling02:24

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 helps...
DNA Microarrays02:34

DNA Microarrays

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...

You might also read

Related Articles

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

Sort by
Same author

Advanced Molecular Analysis in Hemophilia A in a Single Step: Next Generation Sequencing (NGS) and Copy Number Variation (CNV) Analysis.

International journal of laboratory hematology·2026
Same author

A striosomal accumbens pathway drives stereotyped behavior through an aversive Esr1+ hypothalamic-habenula circuit.

Science advances·2025
Same author

Autoreactive T cells identified in patients with anti-Jo1+ antisynthetase syndrome recognise a new epitope on histidyl t-RNA synthetase.

Annals of the rheumatic diseases·2025
Same author

Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling.

Nature communications·2025
Same author

Identification of proliferating neural progenitors in the adult human hippocampus.

Science (New York, N.Y.)·2025
Same author

Efficient profiling of total RNA in single cells with STORM-seq.

bioRxiv : the preprint server for biology·2025
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

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

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

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

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

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

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

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

3D Chromatin Architecture During Early Development: New Methods and New Findings.

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

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

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

Related Experiment Video

Updated: May 27, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

How to analyze gene expression using RNA-sequencing data.

Daniel Ramsköld1, Ersen Kavak, Rickard Sandberg

  • 1Department of Cell and Molecular Biology, Karolinska Institutet and Ludwig Institute for Cancer Research, Stockholm, Sweden.

Methods in Molecular Biology (Clifton, N.J.)
|December 2, 2011
PubMed
Summary
This summary is machine-generated.

RNA sequencing (RNA-Seq) offers superior gene expression analysis over microarrays. This tutorial guides researchers through RNA-Seq data analysis, including gene quantification and novel transcript discovery.

More Related Videos

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Related Experiment Videos

Last Updated: May 27, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Microarrays are currently dominant for gene expression analysis due to established data processing pipelines.
  • RNA sequencing (RNA-Seq) offers superior performance and cost-effectiveness but faces analytical challenges.
  • Despite advancements, widespread RNA-Seq adoption is hindered by complex data analysis requirements.

Purpose of the Study:

  • To provide a tutorial for RNA-Seq data analysis, covering gene expression quantification, splice junction identification, and novel transcript discovery.
  • To enable researchers to perform comprehensive transcriptome analyses using publicly available software.
  • To address the current limitations in RNA-Seq data analysis for organisms with a reference genome.

Main Methods:

  • Utilizing publicly available software for RNA-Seq data analysis.
  • Focusing on transcriptome analysis in organisms with a reference genome.
  • Demonstrating quantification of gene expression, identification of splice junctions, and discovery of novel transcripts.

Main Results:

  • RNA-Seq analysis enables accurate gene expression quantification.
  • Identification of splice junctions and novel transcripts is feasible with current tools.
  • The tutorial facilitates a more accessible approach to RNA-Seq data analysis.

Conclusions:

  • RNA-Seq is a powerful transcriptome analysis method poised to replace microarrays.
  • Standardized and simplified RNA-Seq data analysis pipelines are crucial for its full potential.
  • This tutorial empowers researchers to leverage RNA-Seq for advanced gene expression studies.