Chromium Single Cell Immune Profiling

Multiomic profiling of immune diversity, cell by cell

Chromium Single Cell Immune Profiling provides a multiomic solution to your immunology questions. Analyze full-length, paired B-cell or T-cell receptors, surface protein expression, antigen specificity, and gene expression, all from a single cell.

Single Cell Immune Profiling
  • Multiomic cytometry

    Multiomic cytometry

    Highly sensitive detection of 5’ mRNA with antigen specificity and phenotyping.

  • Complete immune repertoire

    Complete immune repertoire

    Paired, full-length Ig sequence, including isotypes, and T-cell receptor α/β.

  • Immune mapping

    Immune mapping

    Combine immune repertoire with antigen specificity at single cell resolution.

  • Streamlined data analysis

    Streamlined data analysis

    Explore and visualize clonotype information with easy-to-use software.

  • One-day lab workflow

    One-day lab workflow

    From sample to sequencing-ready library in one day, with an option for an automated workflow.

  • Scalable solutions

    Scalable solutions

    From standard experimental needs to higher throughput for comprehensive studies, find the kit that fits your research.

Explore what you can do

  • Discover novel cell types and functions

  • Recover a comprehensive immune repertoire

  • Explore immune receptor mapping

  • Discover new biomarkers

Flexible solutions to meet your needs

Product Family

Single cell resolution for comprehensive immune profiling

Chromium Single Cell Immune Profiling lets you explore the incredible diversity of the innate and adaptive immune system with multiomic readouts and flexibility of scale.

Multiomic analysis

Simultaneously measure cell surface protein expression and antigen specificity with 5’ gene expression.

Immune Repertoire Profiling

Understand clonal expansion and diversity by capturing full-length, paired B-cell and T-cell receptors at a single cell level.

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Immune Repertoire Profiling
  • Paired receptor sequence enables re-expression and testing for antigen binding and function
  • Combined with gene expression data, perform immune cell classification and discover new cell states
Cell Surface Protein

Correlate gene expression measurements with immunophenotyping at a single cell level to better delineate immune cell subsets and functional states.

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Cell Surface Protein
  • Enable ultra-high parameter discovery, using multiomic cytometry to detect up to hundreds of proteins simultaneously with unbiased gene expression profiling
  • Stratify immune cell populations by correlating protein isoforms with regulatory network co-expression in single cells
Antigen Specificity

Assess the specificity of the adaptive immune system at single cell resolution with simultaneous capture of paired T-cell receptors and peptide–MHC multimers, or immunoglobulin heavy and light chains and their cognate antigens.

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Antigen Specificity
  • Explore public and private T-cell antigen specificities using barcoded peptide–MHC multimers
  • Characterize how neoantigens may be targeted by the adaptive immune system
  • Accelerate antibody discovery with a faster and higher throughput screening technology

Large-scale projects

Tackle your most ambitious projects, from rare cell type discovery to translational studies, with our high-throughput (HT) kit and complementary solutions for larger-scale projects.

Single Cell Immune Profiling HT

Transform single cell immune profiling with high-throughput (HT) multiomic analysis on the new Chromium X, and reveal the incredible diversity of the adaptive immune system.

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    Accelerate time to results

    Analyze hundreds of thousands of single cells in a single chip for up to 16 samples at once.

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    Enjoy economy of scale

    Take advantage of high-throughput capabilities and reduce experimental and analysis costs even further with Targeted Gene Expression.

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    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.

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    Built to scale

    Maximize sample throughput and reduce hands-on time by multiplexing libraries during target enrichment.

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    Seamless integration

    Don’t miss any data—seamlessly transition between whole transcriptome and targeted analysis from the same library.

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    More for less

    As studies scale, maximize your budget by decreasing sequencing costs with pre-designed or custom targeted panels.

Workflow automation

Maximize lab productivity and obtain consistent, reproducible results with Single Cell Immune Profiling for Chromium Connect.

Automated Single Cell Immune Profiling

Automate your immune profiling workflow on the Chromium Connect to explore T- and B-cell repertoire diversity, identify rare cell populations, and reveal clonal expansion in response to disease and therapy with increased productivity.

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    Optimize productivity

    Shorten your hands-on time, and go from single cells to sequencing-ready immune profiling libraries with walk-away convenience.

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    Standardize your workflow

    Generate consistent and reproducible single cell immune profiling results across experiments, users, and even across multiple sites.

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    Streamline operations

    Utilize pre-aliquoted, automation-specific reagents that are color-coded and 2D-barcoded for error-proof reagent tracking and loading.

Proven results

Proven results


Watch how customers are using Chromium Single Cell Immune Profiling.

Our end-to-end solution

Chromium instruments with Next GEM technology

Chromium instruments with Next GEM technology

Our scalable instrument

Our compact instrument

Our automated instrument

Chromium Single Cell Immune Profiling reagents

Chromium Single Cell Immune Profiling reagents

With our reagent kits, explore adaptive immunity through multidimensional approaches, including 5’ mRNA, full-length paired BCR and TCR sequences, antigen-receptor specificity, cell surface proteins, and more.

Analysis and visualization software

Analysis and visualization software

Our analysis pipelines

Our visualization software

World-class technical and customer support

World-class technical and customer support

Our expert support team can be contacted by phone or email.


The base workflow for Single Cell Immune Profiling is shown below. If you’re using our Feature Barcoding Kit for Cell Surface Protein or Antigen Specificity, we provide additional protocols for modifying your cells of interest. For the automation option, separate reagents and protocols are available for Chromium Connect.

  1. 1Step 1

    Prepare your sample

    Start with hundreds to hundreds of thousands of cells. Cells can be labeled with antibodies and/or peptide–MHCs conjugated with a unique oligonucleotide barcode. You can use cell suspensions from FACS/MACS, fine needle aspirates, TILs, PBMCs, and more.

  2. 2Step 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.

  3. 3Step 3


    The resulting 10x barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers, for immune and transcriptional profiling of thousands of individual cells.

  4. 4Step 4

    Analyze your data

    Convert raw sequencing data into biologically meaningful insights with Cell Ranger. Cell Ranger processes data from paired immune receptor repertoire sequences, gene expression, and antigen specificity.

    Analysis pipelines output

    Output includes QC information and files that can be easily used for further analysis in our Loupe Browser visualization software or third-party R or Python tools.

  5. 5Step 5

    Visualize your data

    Use our Loupe Browser visualization software to interactively explore your results and compare detailed clonotype information within and across samples and cell types to study gene usage, repertoire diversity, clonal expansion, and more.

    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.


Frequently asked questions

The solution is capable of the modular integration of multiple data types, including mRNA-based whole transcriptome or targeted gene expression, immunophenotyping, adaptive immune repertoire clonality and diversity, and antigen specificity, simultaneously from the same single cells. This multiomic approach to cell characterization helps decipher the rules of the immune system one cell at a time.

Yes. You can amplify only the immunoglobulin or TCR libraries for sequencing and save the amplified whole transcriptome cDNA material for later sequencing.

Chromium Single Cell Immune Profiling is compatible with fresh or cryopreserved single cell suspensions. Typical samples include PBMCs, tumor-infiltrating lymphocytes, spleen, bone marrow cells, and other tissue types. Species can range from human, mouse, rat, and other model organisms. However, only human and mouse are currently supported by 10x Genomics reagents and protocols for immunoglobulin or TCR sequencing.

The Chromium Single Cell Immune Profiling Solution makes use of gene-specific amplification primers that target the constant regions of Ig and TCR genes in order to enrich and sequence across the entire Variable, Diversity, and Joining gene segments.

Yes, immunoglobulin heavy chain sequences are classified by IgA, IgD, IgE, IgM, and IgG.

Single Cell Gene Expression

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