Chromium Single Cell ATAC

Reveal the epigenomic landscape, cell by cell

Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) allows you to analyze chromatin accessibility at the single cell level, providing insights into cell types and states, and deeper understanding of gene regulatory mechanisms.

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Single Cell ATAC

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  • Detect chromatin accessibility

    Analyze thousands of unique open chromatin fragments per cell, genome-wide.

  • Single cell resolution

    Go beyond population averages by measuring epigenomic profiles in single nuclei.

  • Flexible and scalable

    Profile hundreds to tens of thousands of nuclei per chip.

  • Streamlined data analysis

    Explore and visualize chromatin accessibility profiles with easy-to-use software.

  • One-day lab workflow

    From sample to sequencing-ready library in one day.

  • Diverse sample compatibility

    Demonstrated with cell lines, primary cells, and fresh and frozen tissue samples.

Explore what you can do

  • Define cell types and states

  • Characterize regulatory networks

  • Discover cis-regulatory elements, such as promoters and enhancers

  • Reveal associations with treatment response

Proven Results

Watch how customers are using Chromium Single Cell ATAC.

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Find the latest app notes and other documentation Chromium Single Cell ATAC.

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Proven Results

Videos

Watch how customers are using Chromium Single Cell ATAC.

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Publications

Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells

Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells

Science. 2021, Sarropoulos I, et al.

Science. 2021, Sarropoulos I, et al.

Cell-type specialization is encoded by specific chromatin topologies

Cell-type specialization is encoded by specific chromatin topologies

Nature. 2021, Winick-Ng W, et al.

Nature. 2021, Winick-Ng W, et al.

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

Cancer Cell. 2021, Zhang Y, et al.

Cancer Cell. 2021, Zhang Y, et al.

Resources

Find the latest app notes and other documentation Chromium Single Cell ATAC.

Is single cell epigenomics right for me? ATAC-ing your research questions for deeper insights

Is single cell epigenomics right for me? ATAC-ing your research questions for deeper insights

10x Genomics Blog

10x Genomics Blog

Deciphering Epigenetic Regulation with Single Cell ATAC-Seq

Deciphering Epigenetic Regulation with Single Cell ATAC-Seq

Application Note, 10x Genomics

Application Note, 10x Genomics

Single Cell ATAC-Seq for Characterization of Complex Biological Systems

Single Cell ATAC-Seq for Characterization of Complex Biological Systems

Application Note, 10x Genomics

Application Note, 10x Genomics

Our End-to-End Solution

Chromium Instrument with Next GEM technology

Our compact instrument

Our scalable instrument

Chromium Single Cell ATAC Reagents

With our reagent kits, detect open chromatin regions using the included transposase, and generate ready-to-sequence NGS libraries.

Analysis and Visualization Software

Our analysis pipelines

Our visualization software

World-Class Technical and Customer Support

Our expert support team can be contacted by phone or email at [email protected]

Workflow

  1. 1Step 1

    Prepare your sample

    Start with a nuclei suspension isolated from cell culture, primary cells, or fresh or frozen tissue.

    CHROMIUM NUCLEI ISOLATION KIT

    For a wide range of frozen mammalian tissues, the Chromium Nuclei Isolation Kit offers an all-in-one kit for easy and reliable nuclei isolation optimized for the 10x Genomics Single Cell ATAC assay.

    Resources
    • Chromium Nuclei Isolation Kit (expected mid-2022)

    • Demonstrated Protocols
    • Sample Prep Webinar
  2. 2Step 2

    Construct Your 10x Library

    Construct a 10x barcoded library using our reagent kits and a compatible Chromium instrument. Each member of the Chromium instrument family encapsulates each cell with a 10x barcoded Gel Bead in a single partition. Within each nanoliter-scale partition, cells undergo reverse transcription to generate cDNA, which shares a 10x Barcode with all cDNA from its individual cell of origin.

    Resources
  3. 3Step 3

    Sequence

    The resulting 10x Barcoded single cell ATAC-seq library is compatible with standard NGS short-read sequencing on Illumina sequencers, for massively parallel epigenomic profiling of thousands of individual cells.

    Resources
  4. 4Step 4

    Analyze Your Data

    Our Cell Ranger ATAC analysis software generates open chromatin profiles for each cell, identifies clusters of cells with similar profiles and calls peaks, and can aggregate data from multiple samples.

    Analysis Pipelines Output

    Output includes QC information and files that can be easily used for further analysis in our Loupe Browser visualization software, or third-party R or Python tools.

    Resources
  5. 5Step 5

    Visualize Your Data

    Use our Loupe visualization software to interactively explore your results, perform differential accessibility analysis, find clusters enriched for motifs of interest, and compare across samples.

    Do I need to be a bioinformatician to use it?

    Loupe is a point-and-click software that’s easy for anyone to download and use.

    Resources

Frequently Asked Questions

It enables profiling of the open chromatin landscape at single cell resolution.

Yes, using third party tools. For more information, watch our webinar.

Integrative analysis of multi-modal single-cell data

A nuclei suspension is needed. It is possible to obtain high-quality nuclei suspensions from fresh and cryopreserved cells, fresh tissue, and frozen tissue. The Chromium Nuclei Isolation Kit can be used to generate high-quality nuclei suspensions from a wide range of frozen tissues with minimal optimization.

This assay has been optimized for human and mouse samples, although other species may be possible.

Single cell ATAC-seq enables the study of highly heterogeneous samples, identifying unique subpopulations of cell types based on their open chromatin profiles. This could include groups of cells at different developmental stages. Bulk ATAC-seq can only provide an average readout of open chromatin from your sample, potentially masking this cellular heterogeneity.

ATAC-seq captures all open chromatin regions, not just those bound by a specific factor. It is an unbiased (genome-wide) approach to look for epigenetic changes in a sample. For proteins with a known sequence binding motif, the included software can identify those motifs that are enriched in open chromatin on a cell-by-cell basis.

Single Cell Gene Expression

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