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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.
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
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
Kick start your single cell discoveries. Conduct pilot studies, launch initial investigations, or perform sample prep optimization, all with just 500–1,000 cells.
Gain initial insightsWith small-scale investigations, find out what 500–1,000 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 (Next GEM)
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 (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.
- 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.
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.
- 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 (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.
- 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
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 support@10xgenomics.com
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 can be used to interactively explore the results.
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.
