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

Automated biomedical hypothesis generation with time-aware hypergraph contrastive learning.

Knowledge and information systems·2026

Same author

Krüppel-like factor 2 regulates renin expression in mature juxtaglomerular cells.

American journal of physiology. Renal physiology·2026

Same author

Modeling and simulation of neocortical micro- and mesocircuitry (Part I, anatomy).

eLife·2026

Same author

Taming the reference genome jungle: the refget sequence collection standard.

bioRxiv : the preprint server for biology·2025

Same author

Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data.

bioRxiv : the preprint server for biology·2025

Same author

ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation.

Bioinformatics (Oxford, England)·2025

Same journal

Resolving Breakpoints of Chromosomal Rearrangements at the Nucleotide Level Using Sanger Sequencing.

Current protocols in human genetics·2020

Same journal

Informed Consent for Genetic and Genomic Research.

Current protocols in human genetics·2020

Same journal

A Guide to Using ClinTAD for Interpretation of DNA Copy Number Variants in the Context of Topologically Associated Domains.

Current protocols in human genetics·2020

Same journal

The AD Knowledge Portal: A Repository for Multi-Omic Data on Alzheimer's Disease and Aging.

Current protocols in human genetics·2020

Same journal

A Practical Guide for Structural Variation Detection in the Human Genome.

Current protocols in human genetics·2020

Same journal

Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data.

Current protocols in human genetics·2020

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 18, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Analytical Approaches for ATAC-seq Data Analysis.

Jason P Smith^1,2, Nathan C Sheffield^1,2,3,4

¹Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia.

Current Protocols in Human Genetics

|June 17, 2020

Summary

This summary is machine-generated.

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) offers a fast and cost-effective method for studying chromatin accessibility. This primer guides researchers through ATAC-seq data processing and analysis, recommending computational tools for diverse biological questions.

Keywords:

ATAC-seq bioinformatics tools chromatin accessibility data analysis open chromatin pipelines

More Related Videos

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

Published on: March 22, 2019

Related Experiment Videos

Last Updated: Dec 18, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

Published on: March 22, 2019

Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Chromatin accessibility is crucial for understanding gene regulation and DNA-protein interactions.
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a widely adopted method due to its simplicity and cost-effectiveness.
Increasing availability of ATAC-seq data necessitates standardized analysis approaches.

Purpose of the Study:

To provide a foundational understanding of ATAC-seq data processing.
To summarize common analytical methodologies for ATAC-seq data.
To review computational tools and offer recommendations for analyzing ATAC-seq data.

Main Methods:

Explanation of ATAC-seq protocol fundamentals.
Overview of established data processing pipelines.
Review of computational tools for ATAC-seq analysis.

Main Results:

Detailed guidance on ATAC-seq data processing steps.
Categorization of analysis approaches based on research objectives.
Recommendations for selecting appropriate computational tools.

Conclusions:

This primer serves as a starting point for researchers new to ATAC-seq analysis.
It offers a valuable reference for navigating the growing landscape of ATAC-seq data analysis tools and methods.
Effective analysis of ATAC-seq data can address diverse biological questions, from mapping nucleosomes to identifying regulatory elements.