Chromium Single Cell Immune Receptor Mapping

Antigen-specific receptor discovery at scale

Isolate antigen-specific B- and T-cell receptors at scale. Screen the binding specificities of multiple antigens or epitopes for hundreds to hundreds of thousands of B or T cells. Obtain the corresponding paired, full-length receptor sequences for downstream expression and functional testing.

Single Cell Immune Receptor Mapping
  • Scalable antigen screening

    Scalable antigen screening

    Antigen screening of up to hundreds of thousands of T and B cells in a single reaction.

  • Actionable insights

    Actionable insights

    In days, get functional immune receptor sequences alongside antigen specificity.

  • Flexible sample input

    Flexible sample input

    Compatible with magnetic bead–based and flow sorting sample enrichment methods.

  • Compatible partners

    Compatible partners

    Leverage the expertise of our compatible partners for off-the-shelf or custom products.

  • Single integrated workflow

    Single integrated workflow

    From cells to antigen-specific receptor sequences for discovery of novel TCRs or antibodies.

  • Streamlined data analysis

    Streamlined data analysis

    Explore and visualize clonotypes, repertoire diversity, clonal expansion, and more.

Explore what you can do

  • B-cell receptor mapping at scale

  • Gain an understanding of your T-cell repertoire specificity

  • Comprehensive characterization of the immune response to antigens

  • Scale your investigation of antigen specificities with ease

Proven results

Proven results


Watch how researchers are using 10x Genomics products to explore the immune system.

Our end-to-end solution

Chromium instrument with Next GEM technology

Chromium instrument with Next GEM technology

Our scalable instrument

Our compact 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 data processing platform

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.

Components required

Single Cell Immune Receptor Mapping is enabled with the following 10x Genomics products:

Compatible partner products

Immudex dCODE Dextramer® reagents

    BioLegend TotalSeq™ antibodies


    1. 1Step 1

      Prepare your sample

      Label your cells with desired antigens or pMHC multimers conjugated with a unique oligonucleotide barcode. Depending on the expected percentage of antigen-specific cells, cell populations can be enriched through flow-based or magnetic sorting. Compatible cell suspensions include samples from dissociated tumor cells, fine needle aspirates, TILs, PBMCs, and more.

    2. 2Step 2

      Construct your 10x library

      Construct 10x barcoded libraries 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 libraries are 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 to biologically meaningful insights with Cell Ranger. Cell Ranger processes data from gene expression, paired immune receptor repertoire sequences, cell surface proteins, and antigen specificities.

      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 and Loupe V(D)J Browser software to define and compare cell types based on different marker types.

      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

    10x Genomics offers a fully supported workflow for determining antigen-specificity in T cells through use of Immudex’s dCODE Dextramer® reagents. This workflow can identify paired receptors that bind your epitope of interest at the single cell level. A technique recently reported by Vanderbilt can be used to determine B-cell antigen specificity (Ian Setliff et al., High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity. Cell, doi: 10.1016/j.cell.2019.11.003).

    Antigen specificity data can be used for a wide range of assay types, including high-throughput antibody discovery, vaccine design, neo-antigen identification, high-resolution immune profiling studies, and more.

    Most multimer assays are fluorescence-based, meaning that the multimer molecules are tagged with a fluorescent marker that can then be used for sorting antigen-specific cells. These kinds of studies can provide information about the number of antigen-specific cells in a cell population. With Single Cell Immune Profiling, you can get this information, as well the paired, full-length sequences of the antigen-specific receptors and gene expression data at the single cell level. Together, this data provides a complete profile of the immune response.

    Because antigen-specific populations are rare, we recommend sorting for antigen-positive cells prior to 10x Genomics library preparation, but, ultimately, it depends on the goals of the experiment.

    See our Demonstrated Protocol on how to label cells for antigen-specificity staining. Additional resources can be found at the Immudex website.

    Demonstrated Protocol
    Single Cell Gene Expression

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