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

Experimental Design

Experimental Design & Planning

### 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](/products/universal-three-prime-gene-expression)

### 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

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 Gene Expression with CRISPR Screening?

* Understand diverse CRISPR-mediated perturbations at single cell resolution
* [To learn more click here](/products/universal-three-prime-gene-expression)

### 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](/products/universal-three-prime-gene-expression).

### 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 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)

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

Automated library construction with our single cell library prep kit and the Biomek i7 Hybrid workstation combine proven single cell performance with automation excellence to enable you to:

* Prepare sequencing-ready libraries from dozens of samples at once with < 1 hr of hands-on-time, compared to up to 7.5 hours manually
* Automate and scale your studies based on your experimental needs with consistent results across users of different experience levels
* Access deep cellular insights with the same proven performance of our tried-and-trusted manual workflows

Seamless library construction capabilities on automated platforms.

3rd Party Automation

Additional Applications

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

Sample Prep

<Text as={"p"} size={"small"} 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={"small"} weight={"medium"}>{"Demonstrated Protocol Compatibility Table"}</Text></Anchor><Text as={"span"} size={"small"} weight={"regular"}>. GEM-X Single Cell 3' v4 is unsupported with CRISPR Screening and Cell Multiplexing.</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={'small'}>{'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={"small"} 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={"small"} weight={"medium"}>{"Demonstrated Protocol Compatibility Table"}</Text></Anchor><Text as={"span"} size={"small"} 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.