Chromium Single Cell Multiome ATAC + Gene Expression

Unify the Transcriptome and Epigenome in Every Cell

Simultaneously profile gene expression and open chromatin from the same cell with Chromium Single Cell Multiome ATAC + Gene Expression. Multiply your power of discovery to characterize cell types and states, and uncover gene regulatory programs.

Single Cell Multiome ATAC + Gene Expression
  • One cell, two readouts

    One cell, two readouts

    Simultaneous detection of mRNA and chromatin accessibility from the same cell.

  • Define gene regulation

    Define gene regulation

    Discover new gene regulatory interactions.

  • Single cell resolution

    Single cell resolution

    Detect rare cell populations with single cell precision.

  • Flexible and scalable

    Flexible and scalable

    Profile hundreds to tens of thousands of cells per sample.

  • Streamlined data analysis

    Streamlined data analysis

    Explore gene expression and chromatin accessibility simultaneously with easy-to-use software.

  • Efficient lab workflow

    Efficient lab workflow

    From sample to sequencing-ready library in two days.

Uncover hidden insights

Multiomic profiling of the transcriptome and epigenome at single cell resolution can transform your understanding of biology. Enhance your characterization of cell types and states, and gain deeper insights into underlying gene regulatory mechanisms with two readouts from every cell. Get started with Single Cell Multiome ATAC + Gene Expression and multiply your power of discovery.

What You Can Do

Deeper characterization of cell types and states

Characterize complex cell populations and capture cellular heterogeneity to uncover hidden insights with combined epigenomic and gene expression profiling. Leverage gene expression markers to more easily interpret epigenetic profiles.

Discover new gene regulatory interactions

Combine discovery of regulatory elements with gene expression to explore gene regulatory interactions driving cell differentiation, development, and disease.

Make the most of your precious samples

Maximize insights from your limited samples by obtaining transcriptome and open chromatin information from the same cell.

Explore disease complexity

Understand how gene regulatory networks are disrupted in disease. Interrogate epigenetic remodeling and mechanisms of therapeutic resistance.

Our End-to-End Solution

Chromium Instrument with Next GEM technology

Chromium Instrument with Next GEM technology

Our compact instrument

Chromium Single Cell Multiome ATAC + Gene Expression Reagents

Chromium Single Cell Multiome ATAC + Gene Expression Reagents

With our reagent kits, simultaneously detect gene expression and open chromatin regions from the same single cell and generate ready-to-sequence NGS libraries.

Analysis and Visualization Software

Analysis and Visualization Software

Cell Ranger ARC, our analysis pipeline and Loupe Browser, 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.

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  2. 2Step 2

    Construct your 10x library

    Construct paired single cell gene expression and ATAC 10x barcoded libraries 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, mRNA and transposed DNA fragments are labeled with 10x barcodes, where each barcode sequence represents the same unique cell.

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  3. 3Step 3

    Sequence

    The resulting 10x barcoded single cell gene expression and ATAC-seq libraries are compatible with standard NGS short-read sequencing on Illumina sequencers, for massively parallel profiling of thousands of individual cells.

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  4. 4Step 4

    Analyze Your Data

    Our Cell Ranger ARC analysis software generates open chromatin and gene expression profiles for each cell, identifies clusters of cells with similar profiles, and calculates linkages between open chromatin peaks and gene expression.

    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.

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  5. 5Step 5

    Visualize Your Data

    Use our Loupe Browser visualization software to interactively explore your results, compare chromatin accessibility and gene expression across cell types and states, and investigate linkages between open chromatin peaks and gene expression.

    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 simultaneous profiling of the transcriptome (using 3’ gene expression) and epigenome (using ATAC-seq) from single cells to deepen your understanding of how genes are expressed and regulated across different cell types.

In the sample types tested with Single Cell Multiome ATAC + Gene Expression, performance of ATAC and gene expression is comparable to that of the corresponding standalone 10x Genomics workflow (Chromium Single Cell ATAC or Chromium Single Cell Gene Expression) when the starting input is nuclei.

No, currently Feature Barcode technology is not compatible with Single Cell Multiome ATAC + Gene Expression.

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.

Yes, data from Single Cell ATAC and Single Cell Gene Expression is provided in a file format that is compatible with Single Cell Multiome ATAC + Gene Expression and can be integrated using third-party tools, such as Seurat.

Single Cell Gene Expression

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