Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-seq）

Genome-wide profiling of chromatin accessibility to reveal regulatory elements and gene regulatory mechanisms.

ATAC-seq is a high-throughput sequencing method used to analyze genome-wide chromatin accessibility, which is crucial for understanding the global epigenetic regulation of gene expression. Chromatin accessibility refers to the extent to which nuclear macromolecules can interact with chromatinized DNA, enabling transcription and other biological processes. Consequently, ATAC-seq provides valuable insights into the genome’s regulatory landscape by identifying regions where DNA is accessible for binding by various cellular factors.

Benefits of Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-seq）

Flexible Sample Receiving Strategies

Accepts both cells and tissues with low starting amounts.

Profound Experience

Successfully completed hundreds of ATAC-seq projects.

Rapid and High Capacity

Superior turnaround efficiency.

Comprehensive Bioinformatic Analysis

Provides publication-ready results and offers bioinformatic consultants for ATAC-seq data interpretation.

US-based processing

Library preparation, sequencing and customer support in California, Davis.

Applications

Capturing all open chromatin regions under specific space-time conditions, designed to evaluate genome-wide regulatory potential of research goals:

Deciphering Fundamental Biology

Profiling open chromatin in different cell state to decipher cell fate change during cell deveopment, cell differentiate and cellular response.

Understanding Disease Mechanisms

Linking genetic variants to regulatory dysfunction, exploring gene functions in disease progression.

Advancing Drug Discovery & Therapeutics

Profile drug-triggered chromatin regulation to decipher drug efficacy and resistance. Disease-or drug-specific chromatin signatures act as diagnostic and prognostic biomarkers.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

The Novogene ATAC-seq service comprises four steps: Sample preparation, library preparation, sequencing, and bioinformatics analysis. The workflow cannot be paused after sample thawing due to the nature of the initial samples (cells/tissues). Please contact us for more information about your ATAC-seq projects.

To guarantee the accuracy and reliability of sequencing data, Novogene audits every experimental step through quality control, fundamentally ensuring high-quality data output from sampling to the final data report. This commitment to high-quality data is essential for the correctness, comprehensiveness, and credibility of bioinformatics analysis.

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Refer to Data standards – ENCODE for more information about data amount and analysis process for ATAC-seq.

Sample Type	Required Amount (Qubit®)	Shipping Conditions
Frozen Tissue	≥ 50mg (100mg is recommended)	Transport under dry ice conditions
Cryopreserved cell	≥ 500k cells (1M is recommended)，(post-thaw) viability >60%.	Cryopreserved cells (in single cell suspension) should be shipped on dry ice.
Fresh Cell		Fresh cells stored in MACS Cell Storage Buffer, kept in single-cell suspension; Transport on ice packs (no dry ice for fresh cells)

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq Platform
Read Length	Paired-end 150 bp
Recommended Data Amount	9-15 Gb per sample
Content of Data Analysis	Data quality control Mapping Peak calling and statistic Motif analysis Peak annotation and distribution analysis Differential analysis, GO and KEGG enrichment analysis. Visualization of ATAC-seq data

Project Workflow of Novogene ATAC-seq Service

Resources

Demo Results

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Distribution of the Reads Mapped to the Gene Body

Horizontal axis: relative position of the gene. Vertical axis reads density.

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Genome Wide Distribution of Peaks

Horizontal axis is the coordinate of the peak in the chromosome. Vertical is the chromosome. Every blue line represents a peak.

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Motif Analysis

The most significant 25 motifs of length 8, 10, 12, 14 were identified for each set of experiments. More detailed information for each motif is available in the result file and the readme file.

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Distribution of Peaks in Functional Regions

Distribution of peak in different

functional area.

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Enrichment Analysis

Left is a demo graph of GO term enrichment. Right is a demo graph of KEGG pathway enrichment.

Webinars

Introduction to ChIP-seq and ATAC-seq Services: Unveiling Epigenetic Multi-Omics at Novogene

In this webinar, Novogene will provide a comprehensive overview of two powerful epigenetic sequencing products offered by Novogene: ChIP-seq and ATAC-seq. Our expert speaker will discuss the capabilities of these technologies and their potential applications in the field of epigenetics. In addition, Novogene will also present our bioinformatic analysis services, which utilize industry-standard software and programs to provide motif prediction, peak annotation, functional analysis, and data visualization.

NGS Guide – ChIP-Seq and ATAC-Seq

Genome-wide chromatin accessibility is essential for global epigenetic control of gene expression. ATAC-seq is a high-throughput sequencing method for the study of chromatin accessibility. ChIP-Seq combines the selectivity of ChIP with the power of next-generation sequencing (NGS), providing genome-wide profiling of DNA targets for DNA-associated proteins. Our services provide comprehensive solutions starting from library construction to data analysis. Through this webinar, you will be introduced to how these technologies can power your gene expression regulation research and serve as a guide for such sequencing services.

Introduction to ChIP-seq and ATAC-seq Services: Unveiling Epigenetic Multi-Omics at Novogene

NGS Guide – ChIP-Seq and ATAC-Seq

Service flyers

ATAC Service Flyer

More Services

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