High Resolution Profiling of Adaptive Immune Context and Repertoire

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The Chromium Single Cell Immune Profiling Solution

Human or Mouse Immune Cell and Repertoire Profiling at Single Cell Resolution

The Chromium Single Cell Immune Profiling Solution is a comprehensive approach to simultaneously examine the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in human or mouse on a cell-by-cell basis.

From immunology and immuno-oncology research, to infectious disease research and beyond – these solutions, including our intuitive software analysis and visualization tools, will accelerate the understanding of the adaptive immune system.


  • Enrichment for paired, full length human or mouse V(D)J sequences from single T and B cells
  • Whole-transcriptome single cell digital gene expression enables immune cell discovery and phenotypic analysis
  • Simultaneously measure T cell receptor gene, B cell immunoglobulin gene, and gene expression from any sample
  • Profile hundreds to tens of thousands of lymphocytes to detect rare full-length V(D)J transcripts and cell type sub-populations
  • Reveal the clonality, diversity, and cellular context of the immune repertoire using the open-source Cell Ranger Analysis Pipeline, Loupe Cell, and Loupe V(D)J Browsers.

System Features

Rapid and Efficient Microfluidics

  • Partition 100-80,000+ cells in < 7 minutes
  • Run 1 to 8 channels in parallel
  • No lower size limit on cells
  • Recover up to 65% of all loaded cells
  • Low doublet rate: 0.9% per 1,000 cells
  • Compatible with Illumina sequencers
View the Workflow
Single Cell Immune Profiling

Getting Started Guide:
Single Cell Gene Expression

Whether you have questions about how to design your experiments, optimize parameters, or identify the computational/analytical tools necessary to best analyze your single cell gene expression data, this guide has you covered. Take full advantage of the rich information enabled by single cell transcriptomic technology by downloading the getting started guide today!

Download Getting Started Guide

Watch: How It Works

High Resolution Immunology

Learn more about how to identify cell-type-specific immune repertoires on a cell-by-cell basis.

Single Cell Controller

The Chromium Controller

Compact, Sleek, Efficient.

The compact, sleek Chromium Controller has been designed to rapidly and efficiently automate the equivalent of 100,000s to 1,000,000s of pipetting steps for highly parallel sample partitioning and molecular barcoding. The Chromium Controller allows a user to run any of our Chromium Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell CNV, Genome Sequencing and Exome Sequencing Solutions. A dedicated Chromium Single Cell Controller is also available for users that exclusively run our Chromium Single Cell Gene Expression, Single Cell Immune Profiling and Single Cell CNV Solutions.

View Our Controller Gallery

Product List

Gene Expression & Immune Repertoire Profiling

Product Name Product Code
Chromium Single Cell 5′ Library & Gel Bead Kit, 16 rxns 1000006
Chromium Single Cell 5′ Library & Gel Bead Kit, 4 rxns 1000014
Chromium Single Cell A Chip Kit, 48 rxns 120236
Chromium Single Cell A Chip Kit, 16 rxns 1000009
Chromium i7 Multiplex Kit 96 rxns 120262
Chromium Single Cell 5′ Library Construction Kit, 16 rxns* 1000020
Target Enrichment Kits See Enrichment Kits

*Library & Gel Bead Kit contains reagents to generate one library for each reaction. Each additional library from the same sample requires the equivalent number of reactions from the 5′ Library Construction Kit

Immune Repertoire Profiling

Product Name Product Code
Chromium Single Cell 5′ Library & Gel Bead Kit, 16 rxns 1000006
Chromium Single Cell 5′ Library & Gel Bead Kit, 4 rxns 1000014
Chromium Single Cell A Chip Kit, 48 rxns 120236
Chromium Single Cell A Chip Kit, 16 rxns 1000009
Chromium i7 Multiplex Kit 96 rxns 120262
Target Enrichment Kits See Enrichment Kits

Target Enrichment Kits

Species & Target Enrichment Kits Product Code
Human T cells Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, 96 rxns 1000005
Human B cells Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, 96 rxns 1000016
Mouse T cells Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell, 96 rxns 1000071
Mouse B cells Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell, 96 rxns 1000072

Instruments & Analysis

Controllers & Software Product Code
Chromium Single Cell Controller & Accessory Kit, 12 Mo. Warranty 120263
Chromium Single Cell Controller & Accessory Kit, 24 Mo. Warranty 120212
Chromium Controller & Accessory Kit, 24 Mo. Warranty 120246
Chromium Controller & Accessory Kit, 12 Mo. Warranty 120223
Cell Ranger Analysis Pipelines Download Here
Loupe V(D)J Browser Download Here
Loupe Cell Browser Download Here
Single Cell Immune Profiling Datasets
Scientific Seminars

Summer Webinar Series – Single Cell Mouse Immune Profiling

 
  • Giovanna Prout
  • Josephine Lee
10x Genomics
July 26, 2018
Single Cell Summer Webinar Series

Single Cell RNA Sequencing Unveils Mechanisms of Response and Resistance to Immunotherapy

 
  • Aude Chapuis
Fred Hutchinson Cancer Research Center
May 21, 2018
AACR

Single Cell RNA Sequencing Unveils Mechanisms of Response and Resistance to T-Cell Immunotherapy

 
  • Aude Chapuis
Fred Hutchinson Cancer Research Center
February 13, 2018
AGBT

Interrogating the Human Adaptive Immune Response with High-throughput Precision Immunology

 
  • James Crowe
Vanderbilt Vaccine Center
November 21, 2017
Nature Webinar

Harnessing the Therapeutic Potential of Adoptively Transferred Cells

 
  • Aude Chapuis
Fred Hutchinson Cancer Research Center
June 22, 2017
Nature Webcast

Order your Chromium Single Cell Immune Profiling Solution, today.

Request a Quote

Order your 10x system, today.