Chromium Multiomic Cytometry

Ultra-high parameter, single cell multiomic phenotyping

Characterize complex cell suspensions by profiling hundreds of cell surface proteins along with gene expression, at single cell resolution. Gain a high-resolution view of complex biology, cell by cell, and broaden your discovery.

Multiomic Cytometry
  • Ultra-high parameter

    Ultra-high parameter

    Broaden your proteomic discovery by measuring the abundance of hundreds of cell surface epitopes.

  • Multiomics, cell by cell

    Multiomics, cell by cell

    Simultaneously profile mRNA and cell surface proteins, along with TCR/Ig sequences, and antigen specificity.

  • Seamless workflow

    Seamless workflow

    Similar staining procedure to flow cytometry, without spectral overlap or parameter limits.

  • Fast turnaround time

    Fast turnaround time

    Cell staining to sequencing-ready library in as little as one day.

  • Streamlined data analysis

    Streamlined data analysis

    Explore and visualize multiple data types with easy-to-use software.

  • Diverse sample compatibility

    Diverse sample compatibility

    Demonstrated on PBMCs, fresh and frozen cell lines, and dissociated tissue.

Explore what you can do

  • Phenotype complex cell subtypes

  • Identify novel cell types and functions

  • Discover new biomarkers

  • Screen antigen-specific T cells

Proven results

Proven results


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 reagents

Chromium Single Cell reagents

With our reagent kits, obtain a comprehensive multidimensional view of a single cell, including mRNA, cell surface proteins, full-length paired BCR and TCR sequences, and antigen-receptor specificity.

Analysis and visualization software

Analysis and visualization software

Our data processing platform

Our set of 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

Multiomic Cytometry is enabled by the following products from 10x Genomics and its compatible partners.


  1. 1Step 1

    Prepare your sample

    Label your cells with TotalSeq™–B/C antibodies conjugated with a unique oligonucleotide barcode. You can also enrich your populations of interest by staining with antibodies for flow cytometry at the same time. Once the cells are washed, you can proceed to 10x library construction.

  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, cellular transcripts undergo reverse transcription to generate cDNA for both mRNA and cell surface proteins, each of which shares a 10x Barcode with all cDNA from its cell of origin.

  3. 3Step 3


    The resulting 10x barcoded libraries are compatible with standard NGS short-read sequencing on Illumina sequencers for 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 both gene expression and cell surface protein libraries.

    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 tools.

  5. 5Step 5

    Visualize your data

    Use our Loupe Browser to define and compare cell types based on gene expression and cell surface proteins.

    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

In flow cytometry, the number of proteins that can be measured is limited due to inherent spectral overlap, but Feature Barcode technology lets you measure hundreds of parameters without the need for fluorescence compensation. We have compared the distribution of the fluorescence intensity and the UMI counts obtained from flow cytometry and Feature Barcode signals, respectively. Our results have shown that the cell distribution profiles generated by the two technologies are remarkably concordant. Using Multiomic Cytometry, for each cell you can also overlay gene expression, TCR/Ig sequences for T/B cells, and antigen specificity information, allowing accurate characterization of cellular identity, states, and functions.

Application Note: Improving Single Cell Characterization with Simultaneous Gene Expression and Cell Surface Protein Measurements at Scale

It is possible to perform custom conjugation of oligos to antibodies of interest for use with the 10x Genomics workflows. You can use BioLegend's custom conjugation services or Abcam’s custom conjugation kits to obtain or create custom oligo-conjugated antibodies.

Learn more

If you are interested in enriching a certain population of interest or a rare cell type, you can sort your cells before 10x Genomics library preparation. Cells can be stained with oligo-conjugated antibodies along with flow antibodies prior to sorting.

Cell surface protein analysis can be performed without gene expression or immune profiling analysis. Once the cells are stained, they are partitioned into GEMs where cDNA molecules are barcoded. The resulting cDNA are used to generate cell surface protein libraries.

10x Genomics provides analysis and visualization software that includes Cell Ranger, Loupe Browser, and Loupe V(D)J Browser. Cell Ranger is a set of analysis pipelines that automatically generate expression profiles based on genes and/or protein for each cell and identify clusters of cells. The results can then be visualized and interpreted using our interactive visualization software, Loupe Browser and Loupe V(D)J Browser.

Single Cell Gene Expression

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