

| Protocol                                                                                                                                                                                                                                                                                                                      | SC5' V(D)J | SC5' V(D)J with Cell Surface Protein | SC5' V(D)J with 5' CRISPR | SC5' V(D)J with 5' Barcode Enabled Antigen Mapping (BEAM) |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------- | ------------------------------------ | ------------------------- | ------------------------- |
| [Single Cell Protocols - Cell Preparation Guide](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-single-cell-protocols-cell-preparation-guide)                                                                                                                                          | ✓          | ✓                                    | ✓                         |✓                         |
| [Enrichment of CD3+ T Cells from Dissociated Tissues for Single Cell RNA Sequencing and Immune Repertoire Profiling](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-enrichment-of-cd3-t-cells-from-dissociated-tissues-for-single-cell-rna-sequencing-and-immune-repertoire-profiling) | ✓          | ✓\*                                  | ✓\*                       |✓\*        |
| [Tumor Dissociation for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-tumor-dissociation-for-single-cell-rna-sequencing)                                                                                                                                  | ✓\*        | ✓                                    | ✓\*                       |✓\*         |
| [Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/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](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-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](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-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](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-fresh-frozen-human-mouse-cell-line-mixtures-for-single-cell-rna-sequencing)                                                                                | ✓          | ✓                                    | ✓                         |✘  |
| [Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-fresh-frozen-human-peripheral-blood-mononuclear-cells-for-single-cell-rna-sequencing)                                                            | ✓          | ✓                                    | ✓                         |✓ |
| [Cell Surface Protein Labeling for Single Cell RNA Sequencing Protocols](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-cell-surface-protein-labeling-for-single-cell-rna-sequencing-protocols)                                                                                        | ✘          | ✓                                    | ✓                         |✘ |
| [Cell Labeling with dCODE Dextramer® for Single Cell RNA Sequencing Protocols](https://support.10xgenomics.com/single-cell-vdj/sample-prep/doc/demonstrated-protocol-cell-labeling-with-dcode-dextramer-for-single-cell-rna-sequencing-protocols)\*                                                                           | ✘          | ✓                                    | ✘                         |✘ |
| [Isolation of Nuclei for Single Cell RNA Sequencing & Tissues for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-isolation-of-nuclei-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.

Single Cell V(D)J Demonstrated Protocol Compatibility Table

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

Sample Prep

Chromium Single Cell Immune Profiling 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.

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

Chromium X Series

Chromium Controller

Chromium Connect

Single Cell Immune Profiling

Overview

Documentation

Additional Applications

Datasets

Videos

Publications

What is Single Cell Immune Profiling?

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

Cell Surface Protein

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

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.

High Throughput (HT)

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

Barcode Enabled Antigen Mapping (BEAM)

We provide resources from protocols, user guides, and free-to-use analysis tools.

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

Chromium Next GEM Single Cell 5' v2 Dual Index

Chromium Next GEM Single Cell 5' HT v2 Dual Index

Chromium Next GEM Single Cell 5' v1.1 with Feature Barcoding

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.