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 profiles from hundreds to tens of thousands of cells. Explore cellular heterogeneity, identify rare cell types, novel targets, biomarkers, cell types and states.

Single Cell Gene Expression

Single cell resolution at scale

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

Multiomic cellular readout

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

Scalable functional genomics

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

Streamlined data analysis

Explore and interpret single cell gene expression profiles with easy-to-use software.

One-day lab workflow

From sample to sequencing-ready library in one day.

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.

With our comprehensive solutions you get:

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.

Extendable for multiomic readouts

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

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, capture and amplify 3’ mRNA, identify 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. 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 to retrieve high quality single cell suspensions. This minimizes the presence of cellular aggregates and debris.

  2. 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, where all cDNA from individual cells share a common 10x barcode.

  3. 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. 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. 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 you with unbiased, comprehensive single cell transcriptomics profiles from hundreds to thousands of single cells in suspension.

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 2 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.

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

Related Products

Single Cell Gene Expression

Single Cell Immune Profiling

Spatial Gene Expression

Single Cell ATAC

  • 3’ whole transcriptome gene expression
  • Targeted gene expression
  • Paired full-length TCR / BCR sequencing
  • 5’ whole transcriptome gene expression
  • Targeted gene expression
  • 3’ transcriptome gene expression in tissues
  • Epigenomic landscape by open chromatin profiling
  • Cell Surface Protein
  • CRISPR Screening
  • Cell Surface Protein
  • Antigen Specificity
Single Cell Gene Expression

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