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

Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons.

Diabetes & metabolism journal·2026

Same author

Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma.

Journal of extracellular vesicles·2026

Same author

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.

Nature communications·2026

Same author

Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.

Journal of oral microbiology·2026

Same author

A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.

Nature microbiology·2025

Same author

Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.

iScience·2025

Same journal

From Pixels to Patterns: A Multidimensional Framework to Decode Cytoskeletal Organization.

Computational and structural biotechnology journal·2026

Same journal

A Large Concept Model for Mechanistic Simulation of Disease Trajectories: A Hypothesis-Generating Exemplar for Pediatric Acute Lymphoblastic Leukemia.

Computational and structural biotechnology journal·2026

Same journal

Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.

Computational and structural biotechnology journal·2026

Same journal

High-Throughput Prediction of Protein-Protein Interactions Uncovers Hidden Molecular Networks in Biosynthetic Gene Clusters.

Computational and structural biotechnology journal·2026

Same journal

A Region-Aware Structured Framework Improves Prediction of Gene Expression from DNA Methylation.

Computational and structural biotechnology journal·2026

Same journal

Ensemble Machine Learning Approaches Predict Survival in Lower-Grade Glioma Based on Glycosphingolipid Gene Expression and Metabolic Modeling.

Computational and structural biotechnology journal·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 15, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation.

Seungbyn Baek¹, Insuk Lee^1,2

¹Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.

Computational and Structural Biotechnology Journal

|July 9, 2020

Summary

This summary is machine-generated.

Single-cell ATAC-seq (scATAC-seq) reveals cell-specific chromatin accessibility. This review guides analysis of noisy scATAC-seq data, crucial for understanding gene regulation and complex traits.

Keywords:

ATAC sequencing Chromatin accessibility Single-cell ATAC sequencing Single-cell RNA sequencing Single-cell biology

More Related Videos

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

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Related Experiment Videos

Last Updated: Dec 15, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

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

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Area of Science:

Genomics and Epigenetics
Molecular Biology
Bioinformatics

Background:

Genetic variations influencing complex human traits often reside in non-coding genomic regions.
Functional non-coding elements, particularly those involved in epigenetic gene regulation, are key to understanding genotype-phenotype relationships.
Genome-wide chromatin accessibility maps aid in analyzing regulatory elements linked to trait-associated variants.

Purpose of the Study:

To review the single-cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) technology.
To discuss current data analysis methods for scATAC-seq, addressing challenges like data noise and sparsity.
To provide a guideline for effective scATAC-seq data generation and analysis, including software and databases.

Main Methods:

Review of existing literature on scATAC-seq technology and its applications.
Discussion of data preprocessing, analysis, and downstream interpretation techniques for scATAC-seq data.
Compilation of an up-to-date list of studies utilizing scATAC-seq.

Main Results:

Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and its single-cell variant (scATAC-seq) are powerful tools for profiling chromatin accessibility.
scATAC-seq data presents unique challenges due to high noise and sparsity, necessitating advanced analytical approaches.
Various computational methods and software tools have been developed to address these challenges, though a consensus best practice is still emerging.

Conclusions:

This review synthesizes current knowledge on scATAC-seq technology and analysis, offering a valuable resource for researchers.
Effective analysis of scATAC-seq data is critical for extracting biological insights into cell type-specific gene regulation and complex traits.
The provided guidelines aim to facilitate successful scATAC-seq data generation and analysis, promoting advancements in the field.