Introduction

ATAC-Seq (Assay for Transposase-Accessible Chromatin Sequencing) is a powerful epigenomics technique for profiling genome-wide chromatin accessibility. It identifies open chromatin regions that are associated with active promoters, enhancers, transcription factor binding sites, and other regulatory elements involved in gene expression.

Using a hyperactive Tn5 transposase, ATAC-Seq simultaneously fragments accessible DNA and inserts sequencing adapters, enabling rapid library preparation with minimal sample input. Its high sensitivity, speed, and resolution make ATAC-Seq an ideal method for studying gene regulation, cellular differentiation, disease mechanisms, and chromatin dynamics.

How ATAC-Seq Works

ATAC-Seq employs a hyperactive Tn5 transposase to selectively target regions of open chromatin.

The transposase simultaneously:

• • Cleaves accessible DNA regions

• • Inserts sequencing adapters
• • Generates sequencing-ready DNA fragments

• The resulting library is PCR-amplified and sequenced using next-generation sequencing platforms. Bioinformatics analysis then identifies accessible chromatin regions, nucleosome positioning, and regulatory elements across the genome.

Advantages of ATAC-Seq

• • Genome-wide mapping of chromatin accessibility
• • Requires very low sample input
• • Rapid and streamlined library preparation
• • High sensitivity and reproducibility
• • Simultaneous analysis of promoters, enhancers, and regulatory elements
• • Supports transcription factor footprinting and nucleosome positioning
• • Easily integrated with RNA-Seq, ChIP-Seq, and other multi-omics datasets

Applications

• Chromatin Accessibility Profiling

Identify genome-wide open chromatin regions associated with active gene regulation.

• Transcription Factor Analysis

Discover transcription factor binding sites and regulatory networks controlling gene expression.

• Nucleosome Positioning

Map nucleosome occupancy and chromatin organization at high resolution.

• Regulatory Element Identification

Detect promoters, enhancers, silencers, and other functional regulatory regions.

• Disease and Development Research

Investigate epigenetic changes associated with cancer, immune disorders, developmental biology, and other diseases.

• Multi-Omics Integration

Combine ATAC-Seq data with transcriptomics, methylation, or ChIP-Seq datasets for comprehensive regulatory analysis.

ATAC-Seq Workflow

Our optimized ATAC-Seq workflow delivers reliable and reproducible chromatin accessibility profiling.

• Sample preparation and nuclei isolation

• Tn5 transposase-mediated tagmentation

• Library amplification and quality assessment

• High-throughput sequencing

• Bioinformatics analysis, peak calling, transcription factor footprinting, and comprehensive data reporting.

Service Specification

	Sample Requirements Sample type: Human, mouse and rat tissues, Live cells, not genomic DNA. Cell≥ 1 x106, Minimum Quantity: 5 x104 Tissue ≥ 500 mg, Minimum Quantity: 200 mg Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
	Sequencing Strategies Illumina HiSeq PE50 or PE150. For some applications such as nucleosome mapping, paired end sequencing is preferred. Illumina HiSeq PE150. ≥50M Reads.
	Data Analysis We provide multiple customized bioinformatics analyses: Quality control Reference genome mapping Peak calling Annotation Differential analysis Motif discovery Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in ATAC-Seq for your writing (customization)

1. What controls are recommended for an ATAC-Seq experiment?

Appropriate controls are essential for generating reliable and reproducible ATAC-Seq data. Commonly used controls include:

• • Input DNA controls to assess potential biases during library preparation and sequencing.

• • Technical and biological replicates to evaluate reproducibility.
• • Positive controls containing known open chromatin regions to validate assay performance.
• • Negative controls representing closed chromatin regions to assess background signal.

Together, these controls help ensure accurate identification of accessible chromatin regions and improve confidence in downstream analyses.

2. How does ATAC-Seq compare with DNase-Seq and FAIRE-Seq?

ATAC-Seq, DNase-Seq, and FAIRE-Seq are all widely used methods for studying chromatin accessibility, but they differ in workflow and sample requirements.

• • ATAC-Seq uses a hyperactive Tn5 transposase to simultaneously fragment DNA and insert sequencing adapters, providing a rapid, sensitive, and low-input workflow.
• • DNase-Seq identifies accessible chromatin through DNase I digestion but generally requires more starting material and a more complex protocol.
• • FAIRE-Seq isolates nucleosome-depleted DNA using chemical extraction methods but typically offers lower sensitivity than ATAC-Seq.

Due to its simplicity, speed, and ability to work with limited sample quantities, ATAC-Seq has become one of the most widely adopted techniques for genome-wide chromatin accessibility profiling.

3. Which techniques are commonly combined with ATAC-Seq?

ATAC-Seq is frequently integrated with other omics technologies to provide a comprehensive view of gene regulation.

• • ATAC-Seq + RNA-Seq: Correlates chromatin accessibility with gene expression to identify regulatory mechanisms and active pathways.
• • ATAC-Seq + Hi-C: Combines chromatin accessibility with three-dimensional genome organization to investigate how chromatin architecture influences gene regulation.
• • ATAC-Seq + ChIP-Seq: Validates transcription factor binding sites and histone modifications associated with accessible chromatin.
• • ATAC-Seq + Histone Modification Profiling: Integrates chromatin accessibility with activating or repressive histone marks to better understand epigenetic regulation.