Chromium Single Cell

The most versatile single cell toolkit

Chromium Single Cell
Two powerful chemistries to choose from

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Overview
Gene expression

Universal (3' / 5')

Reverse transcription-based whole transcriptome coverage

  • Broadest multiomic options and diverse species compatibility
  • Capture isoforms, long non-coding RNA, and more
  • Highest cell recovery for low-input samples
Gene expression

Flex

Probe-based detection of 18,000+ coding genes

  • Analyze previously inaccessible samples, including fixed tissue and whole blood
  • Robust performance for FFPE and low-quality samples
  • Largest scale and multiplexing: up to 2.56M cells/run
Products
  • Universal 3' Gene ExpressionUniversal 3' Gene Expression
  • Universal 5' Gene ExpressionUniversal 5' Gene Expression
Compatible species
  • AgnosticAgnostic
  • HumanHuman
  • MouseMouse
  • Other species with custom probesOther species with custom probes
Compatible samples
  • Cell suspensionsCell suspensions
  • Nuclei suspensionsNuclei suspensions
  • Flow-sorted cellsFlow-sorted cells
  • Fixed human PBMCsFixed human PBMCs
  • Fresh tissueFresh tissue
  • Frozen tissueFrozen tissue
  • DSP/Methanol-fixedDSP/Methanol-fixed
  • OrganoidsOrganoids
  • Cell suspensionsCell suspensions
  • Nuclei suspensionsNuclei suspensions
  • Flow-sorted cellsFlow-sorted cells
  • Fixed whole bloodFixed whole blood
  • Fresh tissueFresh tissue
  • Frozen tissueFrozen tissue
  • FFPE tissueFFPE tissue
  • PFA-fixed tissuePFA-fixed tissue
  • OrganoidsOrganoids
Multiomic capabilities
  • Gene expressionGene expression
  • TCR & BCR sequencingTCR & BCR sequencing
  • Antigen specificityAntigen specificity
  • Cell surface proteinCell surface protein
  • CRISPR screeningCRISPR screening
  • Chromatin accessibilityChromatin accessibility
  • Gene expressionGene expression
  • Cell surface proteinCell surface protein
  • Intracellular proteinIntracellular protein
  • CRISPR screeningCRISPR screening
Cell & sample throughput

Great for pilot to mid-scale studies

Singleplex
20K cells/sample
160K cells/chip
Output: 8 samples/chip
Hashing
8 channels/chip
60K cells/channel
480K cells/chip
Output: 96+ samples/chip

Maximum scalability

Singleplex
25K cells/sample
160K cells/chip
Output: 8 samples/chip
In-line multiplex
25K cells/sample
2.56M cells/chip
Up to 16 samples/channel
Output: 128 samples/chip
Epigenetics icon
Reveal the epigenomic landscape, cell by cell
Analyze chromatin accessibility at single cell resolution with our Epi kits, resolving cell types and states using genome-wide epigenetic profiles and gaining a deeper understanding of gene regulatory mechanisms.
Use fresh, frozen, or fixed samples—even FFPE samples

Explore open chromatin regions with Assay for Transposase Accessible Chromatin (ATAC-seq) chemistry

Learn about Epi ATAC
Use fresh, frozen, or fixed samples—even FFPE samples

Directly link 3’ gene expression and epigenomic profiles from the same nucleus with the Multiome assay

Learn about Epi Multiome
Use fresh, frozen, or fixed samples—even FFPE samples

Profile up to 80,000 nuclei (1–8 samples) per chip

Use fresh, frozen, or fixed samples—even FFPE samples

Ensure reliable assay performance with an all-in-one isolation kit that requires little to no optimization for most tissues

Learn about the Nuclei Isolation Kit
Compare our most popular Single Cell products
Need help choosing?
Connect with a single cell specialist
chromium
GEM-X Flex Gene Expression
chromium
GEM-X Universal 3' Gene Expression
chromium
GEM-X Universal 5' Gene Expression
GEM-X Flex Gene Expression

Whole transcriptome gene expression, with ultimate flexibility in sample prep and the ability to fix, batch, and run samples on your schedule

We recommend Flex Gene Expression in experiments that...

  • Use archival or lower-quality samples

  • Require flexible sample batching

  • Will scale up and require the lowest cost per-cell

Learn about Flex
Build a Flex Experiment
GEM-X Universal 3' Gene Expression

A versatile solution providing 3' gene expression with options for multiomic analysis

We recommend 3' in experiments that...

  • Require full-length transcript readouts, with or without simultaneous protein expression

  • Only require gene expression, or may use ATAC in the future

  • Have lower cell input requirements

Learn about Universal 3'
Build a Universal 3' Experiment
GEM-X Universal 5' Gene Expression

Comprehensive analysis of immune diversity, combining 5' gene expression with multiomic profiling

We recommend Universal 5' in experiments that...

  • Require full length transcript readouts, with or without simultaneous protein expression

  • Require or may use CRISPR and TCR/BCR sequencing in the future

  • Have lower cell input requirements

Learn about Universal 5'
Build a Univeral 5' Experiment

Primary capability

Probe-based gene expressionProbe-based gene expression

Analyze gene expression using pre-designed probes with the option to add custom probes

3' gene expression3' gene expression

Detect and quantify RNA molecules near the 3' end of genes

5' gene expression5' gene expression

Detect and quantify RNA molecules near the 5' end of genes

Multiomic capabilities

Cell surface proteinCell surface protein

Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions

CRISPR screeningCRISPR screening

Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression

Intracellular proteinIntracellular protein

Achieve detection of proteins throughout the entire cell, including nuclear, cytosolic, and secreted proteins

Cell surface proteinCell surface protein

Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions

Cell surface proteinCell surface protein

Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions

CRISPR screeningCRISPR screening

Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression

TCR/BCR sequencingTCR/BCR sequencing

Understand clonal expansion and diversity by capturing full-length, paired B-cell and T-cell receptors

Antigen specificityAntigen specificity

Interrogate the binding of antigens to immune cell receptors to fully characterize the adaptive immune response.

Compatible species

Human
Human
Mouse
Mouse
Additional species
Additional speciesWith custom probes
Learn more
Human
Human
Mouse
Mouse
Rat
Rat
Non-human primate
Non-human primate
Marine
Marine
Plant
Plant
Insect
Insect
And more
And more
Human
Human
Mouse
Mouse
Rat
RatExcept with TCR/BCR
Non-human primate
Non-human primateExcept with TCR/BCR
And more
And more

Compatible sample types

Cell suspension
Cell suspension
Nuclei suspension
Nuclei suspension
Fresh tissue
Fresh tissue
Frozen tissue
Frozen tissue
FFPE tissue
FFPE tissue
PFA-fixed tissue
PFA-fixed tissue
Flow-sorted cells
Flow-sorted cells
Fixed whole blood
Fixed whole blood
Organoids
Organoids
Cell suspension
Cell suspension
Nuclei suspension
Nuclei suspension
Fresh tissue
Fresh tissue
Frozen tissue
Frozen tissue
Fixed human PBMCs
Fixed human PBMCs
Flow-sorted cells
Flow-sorted cells
Organoids
Organoids
Cell suspension
Cell suspension
Nuclei suspension
Nuclei suspension
Fresh tissue
Fresh tissue
Frozen tissue (gene expression only)
Frozen tissue (gene expression only)
Fixed human PBMCs
Fixed human PBMCs
Flow-sorted cells
Flow-sorted cells
Organoids
Organoids

Resolution

Whole cell/NucleusWhole cell/Nucleus

Cells or nuclei are partitioned into GEM Gel Beads that uniquely barcode each, enabling single cell resolution

Learn about GEM-X Technology
Whole cell/NucleusWhole cell/Nucleus

Cells or nuclei are partitioned into GEM Gel Beads that uniquely barcode each, enabling single cell resolution

Learn about GEM-X Technology
Whole cell/NucleusWhole cell/Nucleus

Cells or nuclei are partitioned into GEM Gel Beads that uniquely barcode each, enabling single cell resolution

Learn about GEM-X Technology

Run configuration options

In-line multiplex

Compatible instruments

Chromium iX and XChromium iX and X

Access our core assays and capabilities with the iX or take advantage of our full single cell portfolio with the Chromium X.

Discover the Chromium X Series
Chromium Xo, iX, and XChromium Xo, iX, and X

Perform 3' gene expression with the low-cost Xo instrument, access our core assays and capabilities with the iX, or take advantage of our full single cell portfolio with the Chromium X.

Discover the Chromium X Series
Chromium iX and XChromium iX and X

Access our core assays and capabilities with the iX or take advantage of our full single cell portfolio with the Chromium X.

Discover the Chromium X Series

Included data processing & analysis software

Cell RangerCell Ranger

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell data on-prem.

Learn about Cell Ranger
Cloud AnalysisCloud Analysis

A platform for running 10x analysis pipelines on optimized cloud clusters for a quick and easy path to results.

Discover Cloud Analysis
Cell RangerCell Ranger

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell data on-prem.

Learn about Cell Ranger
Cloud AnalysisCloud Analysis

A platform for running 10x analysis pipelines on optimized cloud clusters for a quick and easy path to results.

Discover Cloud Analysis
Cell RangerCell Ranger

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell data on-prem.

Learn about Cell Ranger
Cloud AnalysisCloud Analysis

A platform for running 10x analysis pipelines on optimized cloud clusters for a quick and easy path to results.

Discover Cloud Analysis

Included interactive visualization tools

Loupe BrowserLoupe Browser

Visualize and interpret Chromium single cell gene expression data with Loupe Browser, a visualization tool that enables identification of gene expression patterns and cell clusters.

Dive into Loupe Browser
Loupe BrowserLoupe Browser

Visualize and interpret Chromium single cell gene expression data with Loupe Browser, a visualization tool that enables identification of gene expression patterns and cell clusters.

Dive into Loupe Browser
Loupe BrowserLoupe Browser

Interactively explore clonotype information and repertoire diversity alongside gene expression data in Loupe Browser.

Dive into Loupe Browser
Loupe V(D)J BrowserLoupe V(D)J Browser

Investigate clonotypes and examine V(D)J transcripts with this interactive visualization desktop software.

Download Loupe V(D)J

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