### What is Single Cell Gene Expression HT?

- Unbiased single cell 3’ gene expression profiling that enables discovery research
- Simultaneously assess gene expression and protein abundance or perturbation phenotypes from the same cell
- Compatible with sample multiplexing, CRISPR, and targeted gene expression
- Ready-to-use, robust workflow, including demonstrated protocols for various sample types
- Compatible with whole cells and nuclei
- High-throughput sample processing enables ambitious experiments of up to 1M+ cells
- Easy-to-use and convenient software with Cell Ranger analysis pipelines and Loupe Browser visualization tools

### Currently available Feature Barcode kits for Single Cell Gene Expression HT Feature Barcode Technology

|10x Solution|Gene Expression|Cell Surface Protein|CRISPR Screening|CellPlex|
|---------------------------------------------|-|-|-|---|
|Single Cell Gene Expression HT v3.1 (Dual Index)|<Check />|<Check />|<Check />|<Check />|


Profile 2,000–20,000 cells per channel of the Chromium Next GEM Chip M (2,000– 60,000 cells per channel with CellPlex).

Single Cell Gene Expression HT with Feature Barcode technology

High Throughput (HT)

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.

Chromium Next GEM Single Cell 3' HT v3.1 - Dual Index

### What is Gene Expression with Cell Surface Protein Labeling?

- Reveal cell surface protein and gene expression from the same cell
- [To learn more click here](/solutions/single-cell)

### Currently available Feature Barcode kits for Single Cell Gene Expression Feature Barcode Technology

|10x Solution|Gene Expression|Cell Surface Protein|
|---------------------------------------------------------|---|---|
|Single Cell Gene Expression 3' v2|<Check />|-|
|Single Cell Gene Expression 3' v3|<Check />|<Check />|
|Single Cell Gene Expression 3' v3.1|<Check />|<Check />|
|Single Cell Gene Expression 3' v3.1 (Dual Index)|<Check />|<Check />|
|Single Cell Gene Expression 3' HT v3.1 (Dual Index)|<Check />|<Check />|
|Single Cell Gene Expression 3' LT v3.1 (Dual Index)|<Check />|<Check />|



Measure single cell gene and cell surface protein expression simultaneously.

Single Cell Gene Expression with Cell Surface Protein Labeling

Cell Surface Protein

### What is Gene Expression with CRISPR Screening?

* Understand diverse CRISPR-mediated perturbations at single cell resolution
* [To learn more click here](/solutions/single-cell)

### Currently available Feature Barcode kits for Single Cell Gene Expression Feature Barcode Technology

| 10x Solution                                        | Gene Expression | CRISPR Screening |
| --------------------------------------------------- | --------------- | ---------------- |
| Single Cell Gene Expression 3' v2                   | <Check />       | \-               |
| Single Cell Gene Expression 3' v3                   | <Check />       | <Check />        |
| Single Cell Gene Expression 3' v3.1                 | <Check />       | <Check />        |
| Single Cell Gene Expression 3' v3.1 (Dual Index)    | <Check />       | <Check />        |
| Single Cell Gene Expression 3' HT v3.1 (Dual Index) | <Check />       | <Check />        |
| Single Cell Gene Expression 3' LT v3.1 (Dual Index) | <Check />       | \-               |

Assess effects of CRISPR perturbations alongside single cell gene expression.

Single Cell Gene Expression with CRISPR Screening

CRISPR

### What is Gene Expression with Cell Multiplexing technology?

- Utilize species-agnostic, lipid-based tagging compatible with cells or nuclei to load up to 12 samples onto one GEM well. [Click here to learn more](/solutions/single-cell).

### Currently available Feature Barcode kits for Single Cell Gene Expression with Cell Multiplexing Technology

|10x Solution|Gene Expression|Cell Multiplexing|
|----------------------------------------------|---|---|
|Single Cell Gene Expression v2|<Check />|-|
|Single Cell Gene Expression v3|<Check />|-|
|Single Cell Gene Expression v3.1|<Check />|-|
|Single Cell Gene Expression v3.1 (Dual Index)|<Check />|<Check />|
|Single Cell Gene Expression HT v3.1 (Dual Index)|<Check />|<Check />|

Multiplex up to 12 samples per channel for increased sample throughput.

Single Cell Gene Expression with Cell Multiplexing technology

Cell Multiplexing

### What is Single Cell Gene Expression LT?

- Efficiently partitions 100–1,000 cells per channel.
- Simultaneously profile cell surface proteins via Feature Barcode technology.
- Provides a cost-effective way to generate pilot data or optimize sample prep protocols.

### Currently available Feature Barcode kits for Single Cell Gene Expression LT Feature Barcode Technology

|10x Solution|Gene Expression|Cell Surface Protein|CRISPR Screening|CellPlex|
|---------------------------------------------|-|-|-|---|
|Single Cell Gene Expression LT v3.1 (Dual Index)|<Check />|<Check />|-|-|



Partition 100–1,000 cells per channel efficiently, for up to 8,000 cells per run.

Single Cell Gene Expression LT with Feature Barcode technology

Low Throughput (LT)

Chromium Next GEM Single Cell 3' LT v3.1 - Dual Index

Additional Applications

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

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-gene-expression/documentation/steps/sample-prep/compatibility/single-cell-gene-expression-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

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

Targeted

Targeted Gene Expression (Optional)

<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-gene-expression/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.

Single Cell Gene Expression HT with Feature Barcode technology

What is Single Cell Gene Expression HT?

Currently available Feature Barcode kits for Single Cell Gene Expression HT Feature Barcode Technology

Documentation

Software

Videos