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...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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

A single-cell multi-omics assay for simultaneous measurement of vector copy number and protein expression in CAR T cells.

Molecular therapy. Advances·2026
Same author

Interlaboratory assessment of candidate reference materials for lentiviral vector copy number and integration site measurements.

Molecular therapy. Methods & clinical development·2025
Same author

Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing.

Molecular therapy. Methods & clinical development·2025
Same author

Clonal dominance defines metastatic dissemination in pancreatic cancer.

Science advances·2024
Same author

<i>Phyllanthus emblica</i> aqueous extract retards hepatic steatosis and fibrosis in NAFLD mice in association with the reshaping of intestinal microecology.

Frontiers in pharmacology·2022
Same author

Oncogene Overlap Analysis of Circulating Cell-free Tumor DNA to Explore the Appropriate Criteria for Defining MET Copy Number-Driven Lung Cancer.

Clinical lung cancer·2022

Related Experiment Video

Updated: May 23, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.

Onur Sakarya1, Heinz Breu, Milan Radovich

  • 1Life Technologies, Foster City, California, United States of America. osakarya@yahoo.com

Plos Computational Biology
|April 13, 2012
PubMed
Summary
This summary is machine-generated.

We developed an RNA-Seq pipeline to discover low-abundance gene fusions, identifying 40 in breast cancer cells. 36 were validated, with key fusions involving ESR1 and RPS6KB1 found in multiple breast cancer samples.

More Related Videos

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
09:49

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Related Experiment Videos

Last Updated: May 23, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
09:49

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput RNA sequencing (RNA-Seq) allows comprehensive transcript analysis.
  • Detecting low-abundance gene fusions is challenging with short sequencing reads.

Purpose of the Study:

  • To implement an improved RNA-Seq mapping pipeline for accurate gene fusion detection.
  • To identify novel and low-abundance chimeric transcripts in breast cancer.

Main Methods:

  • Development of an RNA-Seq mapping pipeline with novel features like junction mapping and pairing rescue.
  • Integration with a Suffix Array Spliced Read (SASR) aligner for chimeric transcript detection.
  • Paired-end RNA-Seq on the MCF-7 breast cancer cell line using the SOLiD system.

Main Results:

  • Identified 40 gene fusions from over 120,000 splicing junctions.
  • Validated 36 of the 40 identified fusions using TaqMan assays.
  • Discovered recurrent fusions involving ESR1 and RPS6KB1 in breast cancer cell lines and a clinical sample.

Conclusions:

  • The enhanced RNA-Seq pipeline effectively detects low-abundance gene fusions.
  • The identified gene fusions, particularly those involving ESR1 and RPS6KB1, are significant in breast cancer.
  • This approach advances the discovery of fusion transcripts in cancer genomics.