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

Resources:

  • Product Catalog
  • Download Product Sheet
  • Experience 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

View all

Proven results

Videos

Publications

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

Cell Research. Junbin Qian et al., 2020.

Cell Research. Junbin Qian et al., 2020.

Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

Nature Medicine. Yuri Kotliarov et al., 2020.

Nature Medicine. Yuri Kotliarov et al., 2020.

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Nature Biotechnology. Jeffrey M Granja et al., 2019

Nature Biotechnology. Jeffrey M Granja et al., 2019

Resources

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

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

Application Note, 10x Genomics

Application Note, 10x Genomics

Characterization of the Tumor Microenvironment

Characterization of the Tumor Microenvironment

Application Note, 10x Genomics

Application Note, 10x Genomics

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.

Single Cell Immune Profiling

  • Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v2 (1000265, 4 rxns | 1000263, 16 rxns)
  • Chromium Next GEM Single Cell 5’ HT Kit v2 (1000374, 8 rxns | 1000356, 48 rxns)
  • Chromium 5′ Feature Barcode Kit (1000256, 16 rxns)
  • Chromium Next GEM Chip K Single Cell Kit (1000287, 16 rxns | 1000286, 48 rxns)
  • Dual Index Kit TN Set A (1000250, 96 rxns – Protein Libraries)
  • Dual Index Kit TT Set A (1000215, 96 rxns – Gene Expression Libraries)
  • Targeted Gene Expression
  • 10x Compatible BioLegend Total-Seq™–C antibodies
  • 10x Compatible BioLegend TotalSeq™–C Human Universal Cocktail, V1.0
  • 10x Compatible Abcam 5’ Feature Barcode Antibody Conjugation Kit - Lightning-Link®

Single Cell Gene Expression

  • Chromium Next GEM Single Cell 3' Kit v3.1 (1000269, 4 rxns | 1000268, 16 rxns)
  • Chromium Next GEM Single Cell 3’ HT Kit v3.1 (1000370, 8 rxns | 1000348, 48 rxns)
  • Chromium 3’ Feature Barcode Kit (1000276, 16 rxns)
  • Chromium Next GEM Chip G Single Cell Kit (1000127, 16rxns | 1000120, 48 rxns)
  • Dual Index Kit NT Set A (1000242, 96 rxns – Protein Libraries)
  • Dual Index Kit TT Set A (1000215, 96 rxns – Gene Expression Libraries)
  • Targeted Gene Expression
  • 10x Compatible BioLegend TotalSeq™–B antibodies

Workflow

  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.

    Resources
  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.

    Resources
  3. 3Step 3

    Sequence

    The resulting 10x barcoded libraries are compatible with standard NGS short-read sequencing on Illumina sequencers for profiling of thousands of individual cells.

    Resources
  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.

    Resources
  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.

    Resources

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.

Related Products

Products

Single Cell Immune Profiling

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Single Cell Gene Expression

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Spatial Proteomics

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Single Cell ATAC

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Capabilities
  • Paired full-length TCR / BCR sequencing
  • 5’ whole transcriptome gene expression
  • Targeted gene expression
  • 3' whole transcriptome gene expression
  • Targeted gene expression
  • Sample multiplexing
  • 3' whole transcriptome gene expression
  • Epigenomic landscape by open chromatin profiling
Extensions
  • Cell Surface Protein
  • Antigen Specificity
  • Sample multiplexing
  • Cell Surface Protein
  • CRISPR Screening
  • Immunofluorescence protein co-detection
Instruments
  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
  • Chromium X Series
  • Chromium Controller
Single Cell Gene Expression

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