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...
Transcription01:10

Transcription

Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
Transcription01:17

Transcription

Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

You might also read

Related Articles

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

Sort by
Same author

Post-Transcriptional Size-Dependent Expression of the Fission Yeast Cdc13 Cyclin.

bioRxiv : the preprint server for biology·2026
Same author

Extending Biopython to combine multiple sequence alignments with the same reference into a Multiple Sequence Alignment.

microPublication biology·2026
Same author

Genetic and environmental determinants of multicellular-like phenotypes in fission yeast.

Genetics·2026
Same author

Description of <i>Bartonella bennetti</i> sp. nov., a novel rodent-associated species, with comparative genomics of the <i>Bartonella</i> genus.

International journal of systematic and evolutionary microbiology·2026
Same author

PomBase in 2026: expanding knowledge, modeling connections.

Genetics·2026
Same author

Mitochondrial Translation Inhibition Triggers an Rst2-Controlled Transcriptional Reprogramming of Carbon Metabolism in Stationary-Phase Cells of Fission Yeast.

Biomolecules·2025
Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026
Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026
Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026
Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026
Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026
Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026
See all related articles

Related Experiment Video

Updated: Jun 16, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Defining transcribed regions using RNA-seq.

Brian T Wilhelm1, Samuel Marguerat, Ian Goodhead

  • 1Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada.

Nature Protocols
|February 6, 2010
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing enables rapid transcriptome analysis using RNA-seq. This validated protocol details library preparation and bioinformatic analysis for comprehensive gene expression studies.

More Related Videos

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
12:44

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Related Experiment Videos

Last Updated: Jun 16, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
12:44

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) technologies are transforming genomics.
  • NGS allows rapid generation of large DNA sequence data without extensive infrastructure.
  • RNA-sequencing (RNA-seq) applies NGS to characterize entire transcriptomes.

Purpose of the Study:

  • To present a validated protocol for nonstrand-specific transcriptome sequencing using RNA-seq.
  • To describe the library preparation process for RNA-seq.
  • To outline the bioinformatic analysis procedures for RNA-seq data.

Main Methods:

  • Development and validation of a nonstrand-specific RNA-seq protocol.
  • Detailed description of cDNA library preparation steps.
  • Outline of bioinformatic analysis pipeline for transcriptome data.

Main Results:

  • RNA-seq provides high-resolution and deep data for transcriptome characterization.
  • Enables simultaneous gene expression quantification, novel transcript/exon discovery, and splicing efficiency measurement.
  • Validated protocol facilitates efficient transcriptome sequencing.

Conclusions:

  • RNA-seq is a powerful tool for comprehensive transcriptome analysis.
  • While sequencing is rapid (1-2 weeks), downstream bioinformatic analysis is complex and time-consuming (weeks to months).
  • The presented protocol offers a validated approach for nonstrand-specific transcriptome sequencing.