| Protocol                                                                                                                                                                                                                                                                                                                    | HT  | HT with Cell Surface Protein & Immune Receptor Mapping |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | ------------------------------------------------------ |
| [Single Cell Protocols - Cell Preparation Guide](/support/universal-five-prime-gene-expression/documentation/steps/sample-prep/single-cell-protocols-cell-preparation-guide)                                                                                                                                                | ✓   | ✓                                                      |
| [Enrichment of CD3+ T Cells from Dissociated Tissues for Single Cell RNA Sequencing and Immune Repertoire Profiling](/support/universal-five-prime-gene-expression/documentation/steps/sample-prep/enrichment-of-cd-3-plus-t-cells-from-dissociated-tissues-for-single-cell-rna-sequencing-and-immune-repertoire-profiling) | ✓   | ✓\*                                                    |
| [Tumor Dissociation for Single Cell RNA Sequencing](/support/universal-three-prime-gene-expression/documentation/steps/sample-prep/tumor-dissociation-for-single-cell-rna-sequencing)                                                                                                                                       | ✓\* | ✓\*                                                    |
| [Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing](/support/universal-three-prime-gene-expression/documentation/steps/sample-prep/doc/demonstrated-protocol-thawing-dissociated-tumor-cells-for-single-cell-rna-sequencing)                                                                                   | ✓   | ✓\*                                                    |
| [Single Cell Suspensions from Cultured Cell Lines for Single Cell RNA Sequencing](/support/universal-five-prime-gene-expression/documentation/steps/sample-prep/single-cell-suspensions-from-cultured-cell-lines-for-single-cell-rna-sequencing)                                                                            | ✓   | ✓                                                      |
| [Removal of Dead Cells from Single Cell Suspensions for Single Cell RNA Sequencing](/support/universal-five-prime-gene-expression/documentation/steps/sample-prep/removal-of-dead-cells-from-single-cell-suspensions-for-single-cell-rna-sequencing)                                                                        | ✓   | ✓\*                                                    |
| [Fresh Frozen Human-Mouse Cell Line Mixtures for Single Cell RNA Sequencing](/support)                                                                                                                                                                                                                                      | ✓   | ✓                                                      |
| [Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing](/support)                                                                                                                                                                                                                            | ✓   | ✓                                                      |
| [Cell Surface Protein Labeling for Single Cell RNA Sequencing Protocols](/support/universal-five-prime-gene-expression/documentation/steps/sample-prep/cell-surface-protein-labeling-for-single-cell-rna-sequencing-protocols)                                                                                              | ✘   | ✓                                                      |
| [Cell Labeling with Dextramers for Single Cell RNA Sequencing Protocols](/support)\*                                                                                                                                                                                                                                        | ✘   | ✓                                                      |
| [Methanol Fixation of Cells for Single Cell RNA Sequencing](/support/universal-three-prime-gene-expression/documentation/steps/sample-prep/doc/demonstrated-protocol-methanol-fixation-of-cells-for-single-cell-rna-sequencing)                                                                                             | ✘\* | ✘                                                      |
| [Nuclei Isolation from Cell Suspensions & Tissues for Single Cell RNA Sequencing](/support/universal-three-prime-gene-expression/documentation/steps/sample-prep/isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing)                  | ✘\* | ✘                                                      |

✓ Compatible (tested in-house)
✓\* Untested but low risk
✘\* Untested but high risk
✘ Not compatible
\*Antigen-only analysis is not currently supported by 10x Genomics. For antigen analysis, we recommend staining with dextramer reagents in conjunction with a small panel of TotalSeq C antibodies. This increases the cell calling accuracy of the data. Please contact Tech Support for TotalSeq C antibody recommendations.


Lists compatibility of single cell sample preparation Demonstrated Protocols with downstream Chromium Single Cell Immune Profiling assays.

GEM-X technology-powered assays with whole transcriptome coverage to analyze immune diversity 

Universal 5'

Chromium X Series

Chromium

Advanced system for multiomic analysis of hundreds to millions of cells.

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

5' gene expression alongside V(D)J repertoire profiling and antigen specificity of T and B cells.

Immune Profiling HT Demonstrated Protocol Compatibility Table

Prepare optimal single cell/nuclei suspension by following our Demonstrated Protocols.

Sample Prep

Chromium Universal 5' Gene Expression allows analysis of full-length, paired B-cell or T-cell receptor (BCR/TCR) sequences, surface protein expression, antigen specificity, and 5’ gene expression, all from a single cell. Scale up with a high-throughput solution, or focus on key genes with targeted gene expression panels.

Measure single cell gene expression, cell surface protein expression, and optionally antigen specificity simultaneously.

Single Cell Immune Profiling with Cell Surface Protein

Cell Surface Protein

It is critical to choose the User Guide / Protocol that corresponds to your Reagent Kit version. Find the right User Guide via the button below.

Assess the effects of CRISPR perturbations alongside single cell gene expression.

Single Cell Immune Profiling with CRISPR Screening

CRISPR Screening

Enables molecular profiling of 2,000–20,000 cells/sample with simultaneous detection of full length, paired immune receptor sequences, gene and protein expression, and antigen specificity.

Single Cell Immune Profiling HT with Feature Barcode technology

High Throughput (HT)

Chromium Next GEM Single Cell 5' HT v2 Dual Index

Map antigens to discover novel antigen-specific Ig or T-cell receptors.

Single Cell Immune Profiling with Barcode Enabled Antigen Mapping (BEAM)

Barcode Enabled Antigen Mapping (BEAM)

10x PAE Services are designed to help you automate your workflows with confidence.

Premium Automation Enablement (PAE)

Additional Applications

Find resources from protocols to free-to-use analysis tools.

Plan ahead by referring to the list of equipment, kits, and reagents needed for Single Cell Immune Profiling.

Experimental Design

Experimental Design & Planning

Refer to instrument-specific documents for seamless instrument operation.

Instruments

Construct a sequencing-ready single cell library by following our step-by-step User Guide / Protocol.

Library Construction

Use pre-designed or custom panels for targeted gene expression, followed by sequencing and data analysis.

Targeted

Targeted Gene Expression (Optional)

Sequence your single cell library as per our provided recommendations.

Sequencing

Analyze your single cell data using our pipelines, visualization, and Cloud Analysis tools.

Software Analysis

Workflow Documentation

Overview

User Guides

Sample prep

Library prep

Software

Datasets

Videos

Publications

Universal 5' Gene Expression

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Chromium Universal 5' Gene Expression allows analysis of full-length, paired B-cell or T-cell receptor (BCR/TCR) sequences, surface protein expression, and 5’ gene expression, all from a single cell.

What is Universal 5' Gene Expression?

Access free, publicly available data from a number of different sample types generated with Chromium single cell solutions.

GEM-X: How to assemble, load and generate GEMs

GEM-X OCM: How to assemble, load and generate multiplex GEMs

Chromium Next GEM Single Cell 5' v2 Dual Index

Find answers to common technical questions, from sample prep through data analysis, about Chromium single cell workflows.

Q&As

Read key peer-reviewed research publications offering greater insights into biology, enabled by 10x Genomics products and technologies.

Protocol	HT	HT with Cell Surface Protein & Immune Receptor Mapping
Single Cell Protocols - Cell Preparation Guide	✓	✓
Enrichment of CD3+ T Cells from Dissociated Tissues for Single Cell RNA Sequencing and Immune Repertoire Profiling	✓	✓*
Tumor Dissociation for Single Cell RNA Sequencing	✓*	✓*
Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing	✓	✓*
Single Cell Suspensions from Cultured Cell Lines for Single Cell RNA Sequencing	✓	✓
Removal of Dead Cells from Single Cell Suspensions for Single Cell RNA Sequencing	✓	✓*
Fresh Frozen Human-Mouse Cell Line Mixtures for Single Cell RNA Sequencing	✓	✓
Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing	✓	✓
Cell Surface Protein Labeling for Single Cell RNA Sequencing Protocols	✘	✓
Cell Labeling with Dextramers for Single Cell RNA Sequencing Protocols*	✘	✓
Methanol Fixation of Cells for Single Cell RNA Sequencing	✘*	✘
Nuclei Isolation from Cell Suspensions & Tissues for Single Cell RNA Sequencing	✘*	✘