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...

You might also read

Related Articles

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

Sort by

Same author

Integrating transcriptomics and proteomics to assess antisense oligonucleotide safety and efficacy: a time-resolved approach.

NAR molecular medicine·2026

Same author

The prevalence and clinical significance of clonal monocytosis.

Blood·2026

Same author

Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.

Nature communications·2026

Same author

An RBPMS-driven splicing regulatory axis including MBNL1, RBFOX2, and QK promotes smooth muscle cell contractile identity.

Nucleic acids research·2025

Same author

Phased Variant-Supported Circulating Tumor DNA as a Prognostic Biomarker After First-Line Treatment in Large B-Cell Lymphoma: Findings From the DIRECT Study.

Journal of clinical oncology : official journal of the American Society of Clinical Oncology·2025

Same author

Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion.

Nature communications·2025

Search research articles

Related Experiment Video

Updated: Aug 15, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data.

Ilias Moutsopoulos¹, Eleanor C Williams¹, Irina I Mohorianu¹

¹Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK.

Briefings in Bioinformatics

|December 30, 2022

Summary

bulkAnalyseR offers interactive analysis for bulk sequencing data, enhancing exploration and sharing of omics insights. This tool streamlines quality checks, differential expression, and biological interpretation for complex regulatory networks.

Keywords:

ChIPseq bulk sequencing differential expression epigenetics sequencing gene regulatory networks mRNAseq multi-omics integration quality checking

More Related Videos

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Related Experiment Videos

Last Updated: Aug 15, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Area of Science:

Genomics
Bioinformatics
Systems Biology

Background:

Bulk sequencing (single- and multi-omics) is crucial for biological discovery.
Existing analysis methods often lack interactivity and robust integration capabilities.

Purpose of the Study:

To introduce bulkAnalyseR, an R package for interactive analysis of bulk sequencing data.
To provide a user-friendly platform for exploratory data analysis and biological interpretation.

Main Methods:

Utilizes an expression matrix as the primary input.
Integrates state-of-the-art pre-processing, quality-checking, and differential expression analysis functions.
Employs interactive panels for visualization and biological interpretation, including enrichment analyses and regulatory network inference.

Main Results:

Replaces static summary images with dynamic, interactive panels.
Incorporates noise detection in differential expression analysis.
Facilitates robust integration and comparison of various regulatory network modalities (cis-, trans-, customized).

Conclusions:

bulkAnalyseR enhances the exploration and sharing of bulk sequencing data.
The package supports comprehensive analysis from raw data to biological network interpretation.
Enables advanced comparative analysis of complex regulatory interactions across different omics data types.