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

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

  • 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.


Search hundreds peer-reviewed publications using Chromium Single Cell ATAC.


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

Our End-to-End Solution

Chromium Instrument with Next GEM technology

Chromium Instrument with Next GEM technology

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

    World-Class Technical and Customer Support

    World-Class Technical and Customer Support

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


      1. 1

        Prepare your sample

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

      2. 2

        Construct your 10x library

        Construct a 10x barcoded single cell ATAC-seq library using our reagent kits and Chromium Controller. Nuclei are first transposed in bulk, and then encapsulated with a 10x barcoded Gel Bead using the Chromium Controller. Within each nanoliter-scale partition, transposed DNA fragments are labeled with 10x barcodes, where each barcode sequence represents a unique cell.

      3. 3


        The resulting 10x Barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers, for massive transcriptional profiling of thousands of individual cells.

      4. 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 visualization software, or third-party R, or Python tools.

      5. 5

        Visualize Your Data

        Use our Loupe Browser visualization software to interactively explore your results, study expression patterns for genes of interest, determine cell types, and perform comparative analysis between clusters and 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.

      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.

      Related Products

      Single Cell ATAC

      Single Cell Gene Expression

      Single Cell Immune Profiling

      Spatial Gene Expression

      • Epigenomic landscape by open chromatin profiling
      • 3’ whole transcriptome gene expression
      • Targeted gene expression
      • Paired full-length TCR / BCR sequencing
      • 5’ whole transcriptome gene expression
      • Targeted gene expression
      • 3’ transcriptome gene expression in tissues
      • Cell Surface Protein
      • CRISPR Screening
      • Cell Surface Protein
      • Antigen Specificity
      Single Cell ATAC

      Get Started