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.

Single Cell ATAC
  • Detect chromatin accessibility

    Detect chromatin accessibility

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

  • Single cell resolution

    Single cell resolution

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

  • Flexible and scalable

    Flexible and scalable

    Profile hundreds to tens of thousands of nuclei per chip.

  • Streamlined data analysis

    Streamlined data analysis

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

  • One-day lab workflow

    One-day lab workflow

    From sample to sequencing-ready library in one day.

  • Diverse sample compatibility

    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

  • Identify master regulators

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

  • Characterize gene regulatory networks

Proven Results

Proven Results


Watch how customers are using Chromium Single Cell ATAC.

Our End-to-End Solution

Chromium Instrument with Next GEM technology

Chromium Instrument with Next GEM technology

Our compact instrument

Our scalable instrument

Chromium Single Cell ATAC Reagents

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

Analysis and Visualization Software

Our analysis pipelines

Our visualization software

World-Class Technical and Customer Support

World-Class Technical and Customer Support

Our expert support team can be contacted by phone or email.


  1. 1Step 1

    Prepare your sample

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

  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.

  3. 3Step 3


    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.

  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.

  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.


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.

Integration of Multiple Types of Single-Cell Data with Seurat v3

A nuclei suspension is needed. It is possible to obtain high quality nuclei suspensions from fresh and cryopreserved cells, fresh tissue, and frozen tissue. This assay has been optimized for human and mouse samples, although other species may be possible.

Comparisons between bulk ATAC-seq and single cell ATAC-seq from cell lines indicates that single cell ATAC-seq recovers >=90% of peaks recovered by bulk ATAC-seq. Single cell ATAC-seq also provides the resolution to look at chromatin profiles at a cell-type specific level.

ATAC-seq captures all open chromatin regions, not just those bound by a specific factor. It is an unbiased 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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