Single cell resolution at scale
Capture the full heterogeneity of a sample, in hundreds of thousands of cells.
Multiomic cellular readout
Measure 3’ mRNA, cell surface proteins, CRISPR perturbations, and more.
Solutions for any scale
From low-throughput pilot experiments to million-cell studies, find the kit that fits your needs.
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, with flexible options for automated workflows.
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
The standard in single cell gene expression
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.
Gain initial insightsWith small-scale investigations, find out what 100–1,000 cells can reveal.
- Optimize sample prep
Refine experimental conditions to maximize the success of your studies.
- 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
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
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
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.
- Accelerate time to results
Analyze hundreds of thousands of single cells in a single chip for up to 16 samples at once.
- 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.
- 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.
- Built to scale
Maximize sample throughput and reduce hands-on time by multiplexing libraries during target enrichment.
- Seamless integration
Don’t miss any data—seamlessly transition between whole transcriptome and targeted analysis from the same library.
- 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.
- Unlock more insights
Enable greater cell and sample throughput, reducing sample costs and scaling to larger single cell experiments.
- 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.
- 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 workflows on the Chromium Connect to explore cellular heterogeneity, discover novel targets and biomarkers, and unravel complex cellular processes with increased productivity.
- 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.
- Standardize your workflows
Generate consistent and reproducible single cell gene expression results across experiments, users, and even across multiple sites.
- Streamline operations
Utilize pre-aliquoted, automation-specific reagents that are color-coded and 2D-barcoded for error-proof reagent tracking and loading.
Proven Results
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
Science, Apr 2022, Richard K Perez et al.
Science, Apr 2022, Richard K Perez et al.
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
Nature, 2019, Daniel T Montoro, et al.
Nature, 2019, Daniel T Montoro, et al.
Massively parallel digital transcriptional profiling of single cells
Massively parallel digital transcriptional profiling of single cells
Nature Communications, 2017, Grace X Y Zheng, et al.
Nature Communications, 2017, Grace X Y Zheng, et al.
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 Single Cell Gene Expression
Grant Application Resources for Chromium Single Cell Gene Expression
Grant Application Resources, 10x Genomics
Grant Application Resources, 10x Genomics
Single Cell Gene Expression Datasets
Single Cell Gene Expression Datasets
Download our free public datasets
Download our free public datasets
Pushing the Boundaries of Gene Sensitivity with the Chromium Single Cell Gene Expression v3
Pushing the Boundaries of Gene Sensitivity with the Chromium Single Cell Gene Expression v3
Application Note, 10x Genomics
Application Note, 10x Genomics
Our end-to-end solution
Chromium instruments with Next GEM technology
Our scalable instrument
Our compact instrument
Our automated instrument
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
Our data processing platform
Our analysis pipelines
Our visualization software
World-class technical and customer support
Our expert support team can be contacted by phone or email at support@10xgenomics.com
Workflow
Scroll to the right to see the base workflow for Single Cell Gene Expression. 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
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.
Resources - 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.
Resources - 3
Sequence
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.
Resources - 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.
Resources - 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?
Loupe is a point-and-click software that’s easy for anyone to download and use.
Resources
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.
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.
