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

10.6K
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...
10.6K
Ribosome Profiling02:24

Ribosome Profiling

3.7K
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...
3.7K

You might also read

Related Articles

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

Sort by
Same author

Detection of Homologous Recombination Repair Gene Mutations by Tumor Tissue and Circulating Tumor DNA Testing in Prostate Cancer in the Phase III PROpel Trial.

JCO precision oncology·2026
Same author

Runx1 and Runx2 act in concert to suppress Wnt/β-catenin-driven mammary tumourigenesis.

British journal of cancer·2026
Same author

Personalized psoriatic arthritis therapy: the promise of chromosome conformation signatures.

Expert opinion on biological therapy·2026
Same author

Proteomic insights into troponin elevation following COVID-19 infection.

Heart (British Cardiac Society)·2026
Same author

Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

Science advances·2026
Same author

Steroid-dependent metabolic rewiring reveals novel therapeutic and imaging approaches for glioblastoma.

Science advances·2026

Related Experiment Video

Updated: Oct 23, 2025

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
07:29

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

6.3K

Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts.

John J Cole1,2, Bekir A Faydaci3, David McGuinness4

  • 1Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK. John.Cole@glasgow.ac.uk.

BMC Bioinformatics
|August 20, 2021
PubMed
Summary

Searchlight is a new, free pipeline that automates bulk RNA sequencing (RNA-seq) data analysis, visualization, and interpretation. It significantly reduces project time, enabling manuscript-ready figures in under three hours.

Keywords:
AutomationBulkDataExplorationMiningPipelineRNA-seqSignaturesTranscriptomicsVisualisation

More Related Videos

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

982
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

9.9K

Related Experiment Videos

Last Updated: Oct 23, 2025

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
07:29

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

6.3K
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

982
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

9.9K

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Bulk RNA sequencing (RNA-seq) data analysis requires extensive visualization and interpretation after initial processing.
  • Manual analysis using R is time-consuming and laborious.
  • Existing free visualization and interpretation pipelines are limited.

Purpose of the Study:

  • To introduce Searchlight, a freely available pipeline for bulk RNA-seq data visualization and interpretation.
  • To demonstrate Searchlight's capabilities in automating and streamlining the analysis workflow.
  • To compare Searchlight's efficiency against existing tools and manual methods.

Main Methods:

  • Searchlight offers comprehensive statistical and visual analysis at global, pathway, and single-gene levels.
  • It supports diverse experimental designs through three distinct workflows.
  • The pipeline includes report generation and user-friendly R-scripts and a Shiny app for plot customization.

Main Results:

  • Searchlight provides greater automation compared to VIPER and BioJupies.
  • A timed re-analysis study showed Searchlight completes bulk RNA-seq projects to manuscript quality in under 3 hours.
  • The pipeline generates comprehensive statistical and visual analyses.

Conclusions:

  • Searchlight significantly reduces the time and effort for bulk RNA-seq projects compared to manual R analysis or existing free pipelines (VIPER, BioJupies).
  • It is suitable for bioinformaticians, service providers, and bench scientists.
  • The pipeline facilitates the generation of manuscript-level figures efficiently.