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

Introduction to Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-seq)

ATAC-seq is a high-throughput sequencing method for analyzing genome-wide chromatin accessibility, which is essential for understanding the global epigenetic control of gene expression. Sequencing adapters are inserted into open chromatin regions using the hyperactive Tn5 transposase. All open chromatin regions can be captured under a specific space-time condition, without being limited to the binding sites of a transcription factor or a certain histone-modified region.

ATAC-seq Highlights

  • Discover regions of open chromatin by profiling genome-wide active regions.
  • ATAC-seq does not require prior knowledge of regulatory elements.
  • Identify novel enhancers, promoters, and other regulatory elements involved in gene expression and function.
  • The associated analysis is provided to explore correlations between open chromatin regions and transcription factors.

Advantages of ATAC-seq with Novogene

  • Flexible sample receiving strategies: Both cells and tissues can be accepted with low starting amounts.
  • Profound experience: Hundreds of projects successfully completed as of 2023.
  • High capacity: Industry-leading turnaround time.
  • Bioinformatic analysis: Publication-ready results and bioinformatic consultants are available for data interpretation.

Applications of ATAC-seq

  • Cancer research
  • Drug discovery & development
  • Rare & complex diseases
  • Immuno-oncology
  • Stem cells and developmental biology

More Research Services

  • Whole Genome Bisulfite Sequencing (WGBS)
  • Reduced Region Bisulfite Sequencing (RRBS)
  • Chromatin Immunoprecipitation Sequencing (ChIP-seq)

ATAC-seq Specifications: Sample Requirements

Sample Type Required amount Cell viability
Cryopreserved Cells ≥ 500k cells ≥ 60%
Frozen Tissue ≥ 100mg (Recommended)
≥ 50mg (Min)

ATAC-seq Specifications: Sequencing and Analysis

Sequencing Platform Illumina NovaSeq 6000 Sequencing System
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.

Motif Analysis

TMotif indicates the sequence conservation of the position of the peak, which may play a role in the regulation of gene expression.

Note: The most significant 25 motifs of lengths 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.


Distribution of Reads Mapped to the Gene Body

Each gene, along with its 3kb upstream and 3kb downstream regions, is divided into bins according to the window size of 50bp. Full reports include additional analysis results related to the TSS (Transcription Start Site) following peak calling.


Peak Annotation

The distribution of peaks across various functional areas is shown below. The correspondence between peaks and functional areas follows the priority order of promoter, 5’UTR, 3’UTR, Exon, Intron, Downstream, and Intergenic. Additional enrichment analysis is also included in full reports.


Differential Analysis

GO and KEGG enrichment analysis annotate differential peaks between groups enriched in the biological process, cellular component, molecular function, and biological pathway.

Note: Differential analysis can be performed between groups only when there are two or more groups.

*Please contact us to get the full demo report.