Diagenode

ATAC-seq kit

Catalog Number
Format
Price
C01080002
24 rxns
$1,745.00
Other format


ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the transposase Tn5 which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:

  •  Gain insight into gene regulation and understand open chromatin signatures
  •  Determine nucleosome positions at single nucleotide resolution
  •  Uncover transcription factor (TF) occupancy

Diagenode’s ATAC-seq kit is based on a highly validated protocol optimized for 50,000 cells per reaction. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.

ATAC-seq kit features:

  • Cell requirement: 50,000 cells / rxn
  • Robust protocol with high reproducibility between replicates and repetitive experiments
  • Easy and efficient DNA capture after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)
  • Additional qPCR step to determine the number of cycles needed for library amplification:  
    • Avoids over-amplification
    • Allows adaptation/flexibility for more challenging samples to succeed with library prep.
    • Gives early indication if the experiment does not work (no qPCR amplification)

Looking for ATAC-seq on tissue? Please, go to: ATAC-seq package for tissue

  • Method overview

    ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by next generation sequencing, is a key technology to easily identify the open regions of the chromatin. The protocol consists of 3 steps: nuclei preparation, tagmentation and library amplification. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which  cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.

    ATAC-seq kit workflow

  • Example of results

    library prepared with the Diagenode ATAC-seq kit

    Figure 1.Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

    Diagenode ATAC-seq kit

    Figure 2. Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)

    Assay for Transposase-Accessible Chromatin

    Assay for Transposase-Accessible Chromatin

    Figure 3 Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

     open chromatin regions

    Figure 4.
    Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

  •  資料
    ATAC-seq Kit - Manual MANUAL
    Gene expression is carefully regulated in the cells in order to manage a wide range of biological...
    Download
    Chromatin Brochure BROCHURE
    Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has e...
    Download
  •  Safety sheets
    ATAC-seq kit SDS GB en Download
    ATAC-seq kit SDS US en Download
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    ATAC-seq kit SDS JP ja Download
    ATAC-seq kit SDS BE nl Download
    ATAC-seq kit SDS BE fr Download
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    ATAC-seq kit SDS ES es Download
  •  出版物

    How to properly cite this product in your work

    Diagenode strongly recommends using this: ATAC-seq kit (Diagenode Cat# C01080002). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    DNA demethylation triggers cell free DNA release in colorectal cancer cells
    Valeria Pessei et al.
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    Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome
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    Lee M. et al.
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    Kim M. et al.
    During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcr...

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    Sexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistro...

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    Elovitz M. et al.
    The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by Lactobacillus spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including Gardnerella vaginalis, have been associated ...

    Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells
    Liu H. et al.
    Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few ...

    Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates
    Uckelmann M. et al.
    The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomograph...

    UMSBP2 is chromatin remodeler that functions in regulation of geneexpression and suppression of antigenic variation in trypanosomes.
    Soni A. et al.
    Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to co...

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