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.
Create foundational cell atlases and discover new cell types and states with whole transcriptome analysis.
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
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
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
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
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 analysis pipelines
Our visualization software
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.
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.Resources
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
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
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.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 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.
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.