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

ATAC-seq is a high-throughput sequencing technique used for genome-wide chromatin accessibility analysis. It use provides deeper understanding of the complex mechanisms of global epigenetic control over gene expression. The method uses a hyperactive Tn5 transposase to simultaneously fragment and tag open chromatin regions by inserting sequencing adaptors. Subsequent PCR amplification results in the creation of a sequencing library, which allows for the comprehensive identification of open chromatin regions under specific space-time conditions. ATAC-seq provides a holistic view of accessible chromatin landscapes, unlike methods that solely focus on transcription factor binding sites or specific histone-modified regions. By sequencing these open chromatin regions, ATAC-seq reveals regions more likely to active regulatory sequences and potential transcription factor binding sites, offering valuable insights into the dynamic modulation of gene expression across the genome.

Service Details


Demo Results

Featured publications

Service Features

●  Service requires tissue samples, instead of extracted nucleic acids, to conserve the DNA-protein interactions.

●  ATAC method includes tissue dissociation, followed by nuclei isolation, Tn5 treatment and purification, PCR amplification, size selection and sequencing.

● Sequencing in Illumina NovaSeq

Service Advantages

●  High sensitivity: low starting cell quantity is sufficient for library preparation and sequencing.

●  Highly informative technique: simultaneously reveals the genomic locations of open chromatin and active regulatory elements such as transcription factor binding sites.

● Good experimental reproducibility: technical replicates show excellent repeatability. 

● Extensive Expertise: with hundreds of ATAC sequencing projects successfully completed, BMKGENE brings over a decade of experience, a highly skilled analysis team, comprehensive content, and excellent post-sales support.

● Possibility to join with transcriptomics analysis: allowing for the integrated analysis of ATAC seq with other omics data such as RNA-seq.

· Comprehensive bioinformatic analysis: enabling not only the identification of the open regions of the chromatin and their corresponding functionality (promoters, UTs, exons, introns) but also the analysis of differences between chromatin open regions among samples.

Service Specifications


Sequencing Strategy

Recommended data output

Quality control


Illumina PE150

> 20M reads

Depending on genome size (Human: 50 M reads)


Sample Requirements

Samples type: Tissues, live or frozen cells, blood

● Cell number: ≥ 106 cells

● Tissue weight: ≥ 200mg fresh tissue

● Blood: ≥ 4 mL

Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Pilot experiment

DNA extraction

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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    Includes the following analysis:

    ● Raw data quality control;

    ● Peak calling based on mapping to reference genome;

    ● Gene annotation on peak location;

    ● Motif analysis: identification of transcription factor binding sites (TFBS);

    ● Differential Peak Analysis and annotation.

    1.Heatmap on ATAC reads distribution at TSS and adjacent regions (±3 kb)

    3(1)2.Distribution of open chromatin region in different genome components


     3.Differential peak calling between groups


    Explore the research advancements facilitated by BMKGene’s ATAC sequencing services through a curated collection of publications.


    Fu, A. et al. (2023) ‘Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics’, Horticulture Research, 10(1). doi: 10.1093/HR/UHAC228.

    Gong, B. et al. (2023) ‘Epigenetic and transcriptional activation of the secretory kinase FAM20C as an oncogene in glioma’, Journal of Genetics and Genomics, 50(6), pp. 422–433. doi: 10.1016/J.JGG.2023.01.008.

    He, Y. et al. (2023) ‘Butyrate reverses ferroptosis resistance in colorectal cancer by inducing c-Fos-dependent xCT suppression’, Redox Biology, 65, p. 102822. doi: 10.1016/J.REDOX.2023.102822.


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