Chromium Single Cell

Every cell has a story. Tell them all with  Chromium.

Single cell analysis enables meaningful discoveries

Bulk sequencing averages readouts, missing critical details driving complex biology. Single cell sequencing allows scientists to see the unique gene expression patterns of each cell. This view more fully characterizes tissue heterogeneity, revealing the rare cell types that have big consequences in health and disease

Advantage

The Chromium Advantage

Higher gene sensitivity and up to 80% cell recovery efficiency.

Enhanced detection of challenging cell types, including neutrophils.

Reduce hands-on time and lower the risk of errors with instrument-supported automation of the most critical workflow steps.

Produce higher quality libraries that can be sequenced at lower depths.

Backed by 10 years, over 2,200 patents, and >$1.5B in R&D investment.

Innovations

Innovations developed for your success at every step

Our world-class support team is here to boost your success from sample prep to data analysis.
 
 
 

Access more sample types

Profile fresh, frozen, or fixed samples—even FFPE—with optimized protocols for proven performance

Automate critical steps to reduce error

Produce up to 8M barcoded partitions in just minutes, with up to 80% cell recovery

Construct high-quality sequence-ready libraries

Generate libraries with up to 95% usable reads, letting you detect more genes at lower sequencing costs

Analyze & discover with ease

Process and visualize your data with powerful software tools—no bioinformatics experience required

Broad, flexible portfolio of assays

Our world-class support team is here to boost your success from sample prep to data analysis.
 
 
 

Flex

Fix, batch, and run on your schedule.

  • Protein coding gene coverage: Performs well with low-quality and FFPE samples
  • Multiomic readouts from the same cell: Gene expression, Protein, CRISPR
  • Throughput options: Up to 8M cells (1–3,072 samples) per run

Universal

Species agnostic. Maximum versatility.

  • Whole transcriptome coverage: Delivers broadest set of information, including isoforms, SNPs, etc.
  • Multiomic readouts from the same cell: 3' or 5' gene expression, TCR/BCR, Protein, CRISPR
  • Throughput options: Up to 160,000 cells (1–8 samples) per run

Epi Chromatin

Unmask epigenomic profiles.

  • ATAC-seq chemistry: Explore open chromatin regions and link directly to 3' gene expression (Multiome kit)
  • Multiomic readouts from the same cell: Chromatin accessibility, 3' gene expression
  • Throughput options: Up to 80,000 nuclei (1–8 samples) per runUp to 8M cells (1–3,072 samples) per run

During the past years, we observed many advances in single cell technologies thanks to 10x Genomics. This multi-omics approach is very useful for scientists and for physicians to understand human disorders.

David Michonneau, PhD
Professor of Hematology at Saint-Louis Hospital

Meet the Chromium X instrument series

Cell partitioning and barcoding are the most critical steps of your workflow. Chromium X series instruments bring the advantages of automated single cell partitioning to your bench: superior efficiency, reproducibility, and performance with every run.

Scale quickly and seamlessly from small pilots up to 8 million cells per run.

Minimize handling and user errors with fast and automated cell partitioning and barcoding.

Get to results faster with a simple, 1-day workflow—half the time of manual methods.

Options to support the full Chromium portfolio of assays and multiomic capabilities.

Leverage the 10x Genomics Cloud for fast and easy support and software updates.

Access to support with deep technical expertise—from sample prep to data analysis.

Applications

Amplify your research gains

Access the greatest application breadth on the market with superior multiomic integration and 40+ demonstrated protocols.
 
 

Gene expression

Characterize the unique transcriptomic profiles of each cell in your sample

Immune profiling

Obtain functional data for antibody/TCR discovery

CRISPR screening

Directly link CRISPR guide RNAs to the resulting perturbed phenotypes

advantage

Bring the Chromium advantage to your lab

Explore the resources below to learn more about your options and how to get started.
 

Practical considerations and best practices for getting started

Introduction to GEM-X

Grant writing assistance

Buyer's Guide

Platform

Chromium Single Cell

See Chromium products

Visium Spatial

Learn about Visium HD

Xenium In Situ

Learn about Xenium
When to use
Comprehensive single cell data Ideal for deep characterization of cell populations and states.
High-resolution spatial gene expression Understand complex tissues, neighborhoods, and cell to cell interactions. Integration with other spatial-omics, histology, and morphology.
Why to use
Unbiased single cell discovery High per-gene sensitivity
Unbiased spatial discovery
Targeted spatial exploration High per-gene sensitivity
Applications
Whole transcriptome gene expression Protein TCR, BCR CRISPR ATAC
Whole transcriptome gene expression
Targeted gene expression (up to 5,000 genes)
Resolution
Single cell
Transcripts assigned to 2-µm areas
Single cell
Data readout
NGS-based
NGS-based
Imaging-based
Sample compatibility
Single cell or nuclei suspensions from fresh, frozen, or FFPE samples
FFPE Fresh frozen Fixed frozen
Fresh frozen FFPE

Vision Diagnostic

Bring Xenium to your laboratory.

Talk to our scientific and technical team about product selection, panels, applications, pricing and implementation support.