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, surface protein expression, or CRISPR edits in each cell.

Single Cell Gene Expression
  • Single cell resolution at scale

    Single cell resolution at scale

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

  • Multiomic cellular readout

    Multiomic cellular readout

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

  • Solutions for any scale

    Solutions for any scale

    From low-throughput pilot experiments to million-cell studies, find the kit that fits your needs.

  • Streamlined data analysis

    Streamlined data analysis

    Explore and interpret single cell gene expression 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 on fixed, fresh, and frozen samples, as well as whole cells and nuclei.

Explore what you can do

  • Characterize complex cell populations

  • Discover novel cell types and states

  • Unravel complex cellular processes

  • Scalable functional genomics

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 LT

Kick start your single cell discoveries. Conduct pilot studies, launch initial investigations, or perform sample prep optimization, all with just 100–1,000 cells.

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    Gain initial insights

    With small-scale investigations, find out what 100–1,000 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 analysis

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

CRISPR Screening

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

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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    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.

Targeted Gene Expression

Profile a defined set of transcripts to reduce costs while increasing sample number or sequencing depth with customizable, comprehensive gene panels.

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    Built to scale

    Maximize sample throughput and reduce hands-on time by multiplexing libraries during target enrichment.

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    Seamless integration

    Don’t miss any data—seamlessly transition between whole transcriptome and targeted analysis from the same library.

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    More for less

    As studies scale, maximize your budget by decreasing sequencing costs with pre-designed or custom targeted panels.

Sample Multiplexing with 3' CellPlex

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

Automate your gene expression workflow 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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    Optimize productivity

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

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    Standardize your workflow

    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

Proven Results


Watch how customers are using Chromium Single Cell Gene Expression.

Our end-to-end solution

Chromium instruments with Next GEM technology

Chromium instruments with Next GEM technology

Our scalable instrument

Our compact instrument

Our automated instrument

Chromium Single Cell Gene Expression reagents

Chromium Single Cell Gene Expression reagents

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

Analysis and visualization software

Analysis and visualization software

Our data processing platform

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.


The base workflow for Single Cell Gene Expression is shown below. If you’re using 3’ CellPlex or our Feature Barcode Kit for CRISPR Screening or Cell Surface Protein, we provide additional protocols for preparing your samples.

  1. 1Step 1

    Prepare your sample

    Start with hundreds to hundreds of thousands of cells. Follow best practices for washing, counting, and concentrating cells to minimize the presence of cellular aggregates, and retrieve high-quality single cell suspensions.

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

  4. 4Step 4

    Analyze your data

    Our Cell Ranger analysis software generates expression profiles for each cell, identifies clusters of cells with similar profiles, and aggregates 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. 5Step 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 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 only, 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.

Single Cell Gene Expression

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