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

Resources:

  • Product Catalog
  • Product Sheet
  • Single Cell Buyer's Guide
  • 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

View all

Proven Results

Videos

Watch how customers are using Chromium Single Cell ATAC.

Publications

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Nature Biotechnology, 2019, Jeffrey M Granja, et al.

Nature Biotechnology, 2019, Jeffrey M Granja, et al.

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Nature Biotechnology, 2018, Ansuman T Satpathy, et al.

Nature Biotechnology, 2018, Ansuman T Satpathy, et al.

Hic1 Defines Quiescent Mesenchymal Progenitor Subpopulations with Distinct Functions and Fates in Skeletal Muscle Regeneration

Hic1 Defines Quiescent Mesenchymal Progenitor Subpopulations with Distinct Functions and Fates in Skeletal Muscle Regeneration

Cell Stem Cell. 2019, R Wilder Scott, et al.

Cell Stem Cell. 2019, R Wilder Scott, et al.

Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements

Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements

Cell. 2019, Gi Bum Kim, et al.

Cell. 2019, Gi Bum Kim, et al.

Resources

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

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

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.

Workflow

  1. 1Step 1

    Prepare your sample

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

    Resources
  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.

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.

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Capabilities
  • Epigenomic landscape by open chromatin profiling
  • 3' whole transcriptome gene expression
  • Targeted gene expression
  • Sample multiplexing
  • Paired full-length TCR / BCR sequencing
  • 5’ whole transcriptome gene expression
  • Targeted gene expression
  • 3' whole transcriptome gene expression
  • Targeted gene expression
  • Compatible with FFPE and fresh frozen tissue sections
Extensions
  • Sample multiplexing
  • Cell Surface Protein
  • CRISPR Screening
  • Cell Surface Protein
  • Antigen Specificity
  • Spatial Gene Expression with Immunofluorescence
  • Immunofluorescence protein co-detection
Instruments
  • Chromium X Series
  • Chromium Controller
  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
Single Cell Gene Expression

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