The next generation of single cell starts with GEM-X. Check out the Product Sheet for specs and data

Chromium Single Cell Gene Expression

Reveal the full complexity of cellular diversity, cell by cell

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression and multiomic capabilities to profile tens of thousands of cells. Explore cellular heterogeneity, novel targets, and biomarkers with combined gene expression, cell surface protein expression, or CRISPR edits in each cell.

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Single Cell Gene Expression

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  • Single cell resolution at scale

    Capture the full heterogeneity of a sample, in hundreds to tens of thousands of cells.

  • Multiomic cellular readout

    Measure 3’ mRNA, cell surface proteins, CRISPR perturbations, and more.

  • Industry-leading performance

    Be confident in your data, with high cell recovery and sensitive detection of rare transcripts and low RNA-content cells that often evade capture.

  • Streamlined data analysis

    Explore and interpret single cell gene expression profiles with powerful and intuitive software.

  • One-day lab workflow

    From sample to sequencing-ready library in one day, with flexible options for automated workflows.

  • Diverse sample compatibility

    Demonstrated on fresh and frozen samples, as well as whole cells and nuclei.

GEM-X advantage

Increased sensitivity, throughput, data quality, and sample recovery

GEM-X technology drives our next generation of Chromium assays and lays the foundation for more powerful single cell research, now and in the future. Improved microfluidics, assay reagents, and software updates all work together to maximize critical insights.

Learn more about GEM-X technology
10x Chromium Single Cell Gene Expression hardware, software, and reagents.

Up to 2x more genes detected

Substantially increased sensitivity compared to previous versions

2-fold increase in throughput

Built to scale with higher throughput at a lower cost

2-fold reduction in multiplet rate

Enhanced data quality with fewer multiples for a given number of cells

Up to 80% cell capture efficiency

Improved sample recovery makes the most of every run

Flexible solutions to meet your needs

Product Family

The standard in single cell gene expression

Chromium Single Cell Gene Expression can do it all—from handling large-scale projects to discovering the diversity of gene expression, cell by cell.

Initial insights

Get started with single cell gene expression—run pilot studies or optimize future experiments with an affordable solution for small-scale projects.

Single Cell Gene Expression

Kick start your single cell discoveries. Conduct pilot studies, launch initial investigations, or perform sample prep optimization, all with just 500–1,000 cells.

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    Gain initial insights

    With small-scale investigations, find out what 500–1,000 cells can reveal.

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    Optimize sample prep

    Refine experimental conditions to maximize the success of your studies.

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    Support from prep to analysis

    From technical resources to user-friendly, cloud-based data analytics, you are supported end-to-end.

Multiomic profiling

Simultaneously measure cell surface protein expression or CRISPR perturbations with 3’ gene expression.

CRISPR Screening (Next GEM)

Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression.

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CRISPR Screening
  • Screen for novel gene targets or resistance drivers involved in disease
  • Empower functional genetic screens with a faster workflow and increased resolution
  • Unravel the complex genetic regulatory pathways involved in development
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Cell Surface Protein

Explore combined single cell gene and protein expression to enable discovery of novel cell subsets and rare cell populations.

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Cell Surface Protein
  • Enrich distinct cell phenotype understanding with added protein information
  • Explore transcriptome and proteome relationships with simultaneous single cell detection
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Large-scale projects

Tackle your most ambitious projects, from drug screening to pre-clinical trials, with complementary solutions for larger-scale projects.

Single Cell Gene Expression HT (Next GEM)

Expand your experimental possibilities and make million-cell studies routine with high-throughput (HT) gene expression and multiomic analysis on the new Chromium X.

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Learn More About Chromium X
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    Accelerate time to results

    Analyze hundreds of thousands of single cells in a single chip for up to 16 samples at once.

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    Enjoy economy of scale

    Reduce experimental and analysis costs, and complete your most ambitious projects by combining with 3’ CellPlex for sample multiplexing and Targeted Gene Expression.

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    Support from prep to analysis

    From technical resources to user-friendly, cloud-based data analytics, you are supported end-to-end.

Sample Multiplexing with 3' CellPlex (Next GEM)

Lower your cost per sample as the scale of your studies increases with an end-to-end sample multiplexing solution, and pair with our HT kit to bring million-cell experiments within reach.

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    Unlock more insights

    Enable greater cell and sample throughput, reducing sample costs and scaling to larger single cell experiments.

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    Broad sample compatibility

    Multiplex samples with a single set of reagents compatible across samples and species, including patient samples, animal models, cell lines, and whole cells or nuclei.

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    End-to-end solution

    Leverage fully supported protocols and integrated data analysis pipelines with demultiplexing capabilities to efficiently enable large-scale single cell experiments.

Workflow automation

Maximize lab productivity and obtain consistent, reproducible results with Single Cell Gene Expression for Chromium Connect.

Automated Single Cell Gene Expression (Next GEM)

Automate your gene expression workflows on the Chromium Connect to explore cellular heterogeneity, discover novel targets and biomarkers, and unravel complex cellular processes with increased productivity.

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Learn More About Chromium Connect
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    Optimize productivity

    Shorten your hands-on time, and go from single cells/nuclei or cDNA to sequencing-ready gene expression libraries with walk-away convenience.

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    Standardize your workflows

    Generate consistent and reproducible single cell gene expression results across experiments, users, and even across multiple sites.

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    Streamline operations

    Utilize pre-aliquoted, automation-specific reagents that are color-coded and 2D-barcoded for error-proof reagent tracking and loading.

Proven Results

Explore our videos on Chromium Single Cell Gene Expression.

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Find the latest app notes and other documentation for Chromium Single Cell Gene Expression.

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Proven Results

Videos

Explore our videos on Chromium Single Cell Gene Expression.

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Publications

Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Richard K Perez, et al. Science (2022).

Richard K Perez, et al. Science (2022).

Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology

Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology

Hansruedi Mathys, et al. Cell (2023).

Hansruedi Mathys, et al. Cell (2023).

An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis

An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis

Shuang Wang, et al. Science Translational Medicine (2023).

Shuang Wang, et al. Science Translational Medicine (2023).

Resources

Find the latest app notes and other documentation for Chromium Single Cell Gene Expression.

Getting Started with Gene Expression Guide

Getting Started with Gene Expression Guide

Experiment Planning Guide, 10x Genomics

Experiment Planning Guide, 10x Genomics

Grant application resources for Chromium GEM-X Single Cell Gene Expression

Grant application resources for Chromium GEM-X Single Cell Gene Expression

Grant Application Resources, 10x Genomics

Grant Application Resources, 10x Genomics

The neXt generation of single cell starts with GEM-X

The neXt generation of single cell starts with GEM-X

GEM-X Single Cell Flyer, 10x Genomics

GEM-X Single Cell Flyer, 10x Genomics

Our end-to-end solution

Chromium instruments with GEM-X technology

The Chromium X handles all single cell assays, low to high throughput.

Chromium Single Cell Gene Expression reagents

With our reagent kits, explore cellular diversity through 3’ mRNA, cell surface proteins, CRISPR perturbations, and more.

Intuitive analysis and visualization software

Discover single cell analysis, including cloud data processing, Cell Ranger analysis pipelines, and Loupe, our visualization app.

World-class technical and customer support

Contact our expert support team at [email protected]

Frequently asked questions

It provides a comprehensive way to profile gene expression, either whole transcriptome or targeted, alongside Cell Surface Protein or CRISPR edits for multidimensional insights into complex biology.

Any cell type that expresses polyadenylated mRNA molecules is compatible with this single cell RNA-seq workflow.

Chromium Single Cell Gene Expression is compatible with fresh, fixed (methanol), and cryopreserved single cell or single nuclei suspensions. Species can range from human, mouse, rat, model organisms, and plants.

10x Genomics Cloud Analysis enables you to process your single cell gene expression data through a simple web interface, leveraging an optimized, scalable infrastructure for fast results. Users can set up and run Cell Ranger pipelines through Cloud Analysis. Cell Ranger is a set of analysis pipelines that will automatically generate expression profiles for each cell and identify clusters of cells with similar expression profiles. Subsequently, Loupe Browser, a visualization software, can be used to interactively explore the results. Cloud Analysis is currently available in the US, Canada, and Europe, but you can freely download both Cell Ranger and Loupe Browser from our support site and analyze 10x Genomics datasets on your own compute environment.

See 10x Support

Internally, we have tested cells of up to 30 microns in size. In addition, a number of customer publications have successfully demonstrated the use of cell types, such as hepatocytes, fibroblasts, and cardiomyocytes, that are typically well beyond 30 microns in size.

Next GEM and GEM-X chips both efficiently generate Gel Beads-in-emulsion (GEMs) as part of the Chromium workflow. However, GEM-X chips use new technology that provides higher performance, with architecture, settings, and partition size all optimized based on a wealth of experience from Next GEM and Legacy assays. GEM-X chips run exclusively on our Chromium X and iX instruments, which support the full breadth of our Chromium assays.

Single Cell Gene Expression

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