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 tens of thousands of cells.

  • Multiomic cellular readout

    Multiomic cellular readout

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

  • Scalable functional genomics

    Scalable functional genomics

    Explore gene networks with paired CRISPR knockdowns and whole transcriptome readouts.

  • 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 Targeted and Whole Transcriptome Assays

Explore cellular phenotypes with whole transcriptome analysis or focus on your genes of interest using targeted gene expression panels.

Targeted Gene Expression Panels

Choose from pre-designed cancer, immunology, neuroscience and gene signature panels with the ability to add up to 200 custom genes, or design fully custom panels.

Powerful discovery

Create foundational cell atlases and discover new cell types and states with whole transcriptome analysis.

Seamless integration

Validate discoveries or explore new hypotheses with the ability to transition seamlessly between whole transcriptome and targeted analysis from the same library preparation.

More for less

Scale your studies or maximize your budget using targeted panels to decrease sequencing costs.

Capabilities for multiomic readouts

Cell Surface Protein

Feature Barcode Technology

Cell Surface Protein

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

  • Enrich distinct cell phenotype understanding with added protein information
  • Explore transcriptome and proteome relationships with simultaneous single cell detection
CRISPR Screening

Feature Barcode Technology

CRISPR Screening

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

  • 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

Proven Results

Proven Results


Watch how customers are using Chromium Single Cell Gene Expression.


Search over 600 peer-reviewed publications using Chromium Single Cell Gene Expression


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

Our End-to-End Solution

Chromium Instrument with Next GEM technology

Chromium Instrument with Next GEM technology

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 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 our Feature Barcode Kit for CRISPR or Cell Surface Protein, we provide additional protocols for modifying your cells of interest.

  1. 1Step 1

    Prepare your sample

    Start with hundreds to 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 Chromium Controller. The Chromium Controller 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 provides two types of software that will help you analyze your data: Cell Ranger and Loupe Browser. Cell Ranger is an analysis software which will automatically generate expression profiles for each cell and identify clusters of cells with similar expression profiles. You can then use Loupe Browser, a visualization software, to interactively explore the results. You can download Cell Ranger and Loupe Browser from the 10x Support site at no cost.

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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