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

Targeted

Targeted Gene Expression (Optional)

### What is Immune Profiling with Feature Barcode technology for Cell Surface Protein?

* Reveal immune repertoire, gene expression and cell surface protein from the same cell
* [To learn more click here](/solutions/vdj)

### Currently available Feature Barcode kits for Single Cell Immune Profiling

| 10x Solution                                                                             | TCR/Ig    | Gene Expression | Cell Surface Marker | Immune Receptor Mapping with dCODE™ Dextramer® | CRISPR    | Barcode Enabled Antigen Mapping (BEAM) |
| ---------------------------------------------------------------------------------------- | --------- | --------------- | ------------------- | ---------------------------------------------- | --------- | -------------------------------------- |
| Single Cell Immune Profiling                                                             | <Check /> | <Check />       | \-                  | \-                                             | \-        | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein                                   | <Check /> | <Check />       | <Check />           | <Check />                                      | \-        | \-                                     |
| Single Cell Immune Profiling with CRISPR screening                                       | <Check /> | <Check />       | \-                  | \-                                             | <Check /> | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein & CRISPR                          | <Check /> | <Check />       | <Check />           | \-﻿                                            | <Check /> | \-                                     |
| Single Cell Immune Profiling with Barcode Enabled Antigen Mapping                        | <Check /> | <Check />       | \-﻿                 | \-                                             | \-        | <Check />                              |
| Single Cell Immune Profiling with Cell Surface Protein & Barcode Enabled Antigen Mapping | <Check /> | <Check />       | <Check />           | \-﻿                                            | \-        | <Check />                              |

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.

### What is 5' CRISPR?

Single Cell 5' CRISPR Screening (also referred to as 5' CRISPR) enables whole transcriptome readouts for gene perturbations, along with cell surface protein and immune receptor sequences, all from the same single cell.

- [To learn more click here](/products/single-cell-crispr-screening)

### Currently available Feature Barcode kits for Single Cell Immune Profiling 

| 10x Solution                                                                             | TCR/Ig    | Gene Expression | Cell Surface Marker | Immune Receptor Mapping with dCODE™ Dextramer® | CRISPR    | Barcode Enabled Antigen Mapping (BEAM) |
| ---------------------------------------------------------------------------------------- | --------- | --------------- | ------------------- | ---------------------------------------------- | --------- | -------------------------------------- |
| Single Cell Immune Profiling                                                             | <Check /> | <Check />       | \-                  | \-                                             | \-        | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein                                   | <Check /> | <Check />       | <Check />           | <Check />                                      | \-        | \-                                     |
| Single Cell Immune Profiling with CRISPR screening                                       | <Check /> | <Check />       | \-                  | \-                                             | <Check /> | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein & CRISPR                          | <Check /> | <Check />       | <Check />           | \-﻿                                            | <Check /> | \-                                     |
| Single Cell Immune Profiling with Barcode Enabled Antigen Mapping                        | <Check /> | <Check />       | \-﻿                 | \-                                             | \-        | <Check />                              |
| Single Cell Immune Profiling with Cell Surface Protein & Barcode Enabled Antigen Mapping | <Check /> | <Check />       | <Check />           | \-﻿                                            | \-        | <Check />                              |

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

Single Cell Immune Profiling with CRISPR Screening

CRISPR Screening

### What is Single Cell Immune Profiling HT?

* Profile 2,000 to 20,000 single cells to detect rare clonotypes and cell type sub-populations per sample
* Simultaneously characterize gene expression and enrich for single TCR and Ig cells providing paired, full length V(D)J receptor sequences in the same cells 
* Simultaneously measure additional biological information with Feature Barcode technology 

  * Perform Barcode Enabled Antigen Mapping (BEAM) to link full-length, paired V(D)J sequences with antigen specificity
  * Simultaneously measure cell surface protein expression
  * Directly connect CRISPR guides to their gene expression perturbation profiles
* Easy to install and use pipelines and visualization software

### Currently available Feature Barcode kits for Single Cell Immune Profiling HT Feature Barcode Technology

| 10x Solution                      | Gene Expression | Cell Surface Protein & Immune Receptor Mapping | CRISPR Screening | CellPlex | Barcode Enabled Antigen Mapping |
| --------------------------------- | --------------- | ---------------------------------------------- | ---------------- | -------- | ---------- |
| Single Cell 5' HT v2 (Dual Index) | <Check />       | <Check />                                      | <Check />        | \-       | <Check /> |

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

### What is Barcode Enabled Antigen Mapping (BEAM)?

* BEAM enables mapping antigens to discover novel antigen-specific Ig or T cell receptors

  * [To learn more click here](/products/single-cell-barcode-enabled-antigen-mapping)

### Currently available Feature Barcode kits for Single Cell Immune Profiling

| 10x Solution                                                                             | TCR/Ig    | Gene Expression | Cell Surface Marker | Immune Receptor Mapping with dCODE™ Dextramer® | CRISPR    | Barcode Enabled Antigen Mapping (BEAM) |
| ---------------------------------------------------------------------------------------- | --------- | --------------- | ------------------- | ---------------------------------------------- | --------- | -------------------------------------- |
| Single Cell Immune Profiling                                                             | <Check /> | <Check />       | \-                  | \-                                             | \-        | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein                                   | <Check /> | <Check />       | <Check />           | <Check />                                      | \-        | \-                                     |
| Single Cell Immune Profiling with CRISPR screening                                       | <Check /> | <Check />       | \-                  | \-                                             | <Check /> | \-                                     |
| Single Cell Immune Profiling with Cell Surface Protein & CRISPR                          | <Check /> | <Check />       | <Check />           | \-﻿                                            | <Check /> | \-                                     |
| Single Cell Immune Profiling with Barcode Enabled Antigen Mapping                        | <Check /> | <Check />       | \-﻿                 | \-                                             | \-        | <Check />                              |
| Single Cell Immune Profiling with Cell Surface Protein & Barcode Enabled Antigen Mapping | <Check /> | <Check />       | <Check />           | \-﻿                                            | \-        | <Check />                              |

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)

Additional Applications

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

Experimental Design

Experimental Design & Planning

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

Sample Prep

<Text as={"p"} size={"medium"} style={{ lineHeight: "28px"}} weight={"regular"}>To check if a Demonstrated Protocol is compatible with a specific chemistry version, refer to the <Anchor href={"/support/single-cell-immune-profiling/documentation/steps/sample-prep/compatibility/single-cell-v-d-j-demonstrated-protocol-compatibility-table"}><Text as={"span"} color={"inherit"} size={"medium"} weight={"medium"}>{"Demonstrated Protocol Compatibility Table"}</Text></Anchor><Text as={"span"} size={"medium"} weight={"regular"}>.</Text></Text>

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

<DocumentCallout><Text as={'p'} size={'medium'}>{'After June 30, 2023, new Cell Ranger and Space Ranger releases will no longer support targeted gene expression analysis.'}</Text></DocumentCallout><Text as={"p"} size={"medium"} style={{ lineHeight: "28px"}} weight={"regular"}>To check if a Demonstrated Protocol is compatible with a specific chemistry version, refer to the <Anchor href={"/support/single-cell-immune-profiling/documentation/steps/targeted-gene-expression/targeted-gene-expression-protocol-compatibility-table"}><Text as={"span"} color={"inherit"} size={"medium"} weight={"medium"}>{"Demonstrated Protocol Compatibility Table"}</Text></Anchor><Text as={"span"} size={"medium"} weight={"regular"}>.</Text></Text>

Sequence your single cell library as per our provided recommendations.

Sequencing

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