Targeted Gene Expression

Focus on the Genes that Matter Most

Profile a defined set of transcripts from single cells or tissue sections with Targeted Gene Expression. Reduce costs while increasing the number of samples, or increasing sequencing depth with customizable, comprehensive gene panels.

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Targeted Gene Expression



After June 30, 2023, new Cell Ranger and Space Ranger releases will no longer support targeted gene expression analysis.

  • More for less

    Cut sequencing costs by as much as 90%, or scale up to a 10-fold increase in sample throughput compared to whole transcriptome analysis.

  • Increase flexibility

    Work with pre-designed panels, add genes or sequences on top, or design your own panel from scratch.

  • Stay on target

    Don’t miss any important genes. Maximize on-target reads and minimize data volume.

  • Seamless integration

    Easily integrate with Feature Barcode technology and any existing gene expression libraries.

  • Built to scale

    Easily scale sample throughput by multiplexing libraries during target enrichment.

  • Streamlined data analysis

    Explore and interpret targeted gene expression profiles with easy-to-use software.

Accelerate translational research

Move faster and inform translational studies with actionable data by focusing on clinically relevant gene expression.

Scale cellular screening

Enable genetic screens at massive scale for CAR-T cell characterization or CRISPR gene editing.

Refine discoveries

Detect and localize rare or unique cellular populations to gain deeper insights into normal development and disease pathology.

Validate biomarkers and drug targets

Use whole transcriptome analysis for discovery, then seamlessly enrich the same libraries for the most relevant genes.

Panel Options

Pre-designed Panels

Hone in on gene expression relevant to your research area. Each panel consists of validated probes for over 1,000 genes.

Human Pan-Cancer Panel
Human Immunology Panel
Human Gene Signature Panel
Human Neuroscience Panel

Add on to Pre-designed Panels

Customize pre-designed panels by adding up to 200 additional genes and up to 10 exogenous sequences with the 10x Genomics Custom Panel Designer.

Create Fully Custom Panels

If you’d like to start from scratch and tackle a different research area, or you have a specific set of mouse or human genes you want to analyze, the Custom Panel Designer will create those designs and help you get started.

How the Custom Panel Designer Works

Create an account

Design custom panels and save them to your account.

Select your panel type

Start with one of our pre-designed panels and add custom genes or design a fully custom panel.

Input custom gene list

Add up to 200 genes and 10 exogenous sequences to pre-designed panels or create a fully custom panel of 10–1,500 genes.

Review and download design files

Once you’re happy with your design, request a quote for 10x Genomics reagents and order your custom panel from our compatible partner.

Scalable studies with sample multiplexing

Increase your understanding of biological complexity by implementing single cell studies at scale with an end-to-end sample multiplexing solution.

Single Cell Gene Expression with CellPlex

Utilize species-agnostic, lipid-based tagging compatible with cells or nuclei to multiplex up 12 samples.

Unlock more insights

Enable greater cell and sample throughput with multiplexing, reducing sample costs and scaling to larger single cell experiments.

Broad sample compatibility

Multiplex samples with a single set of reagents compatible across samples, including patient samples, cell lines, and whole cells or nuclei.

End-to-end solution

Leverage fully supported protocols and integrated data analysis pipelines with demultiplexing capabilities to efficiently enable large-scale single cell experiments.

Customization options

View what custom panel options are available for different products and references below.

Product Configuration
Panel Options
ProductReferencePre-designed PanelsAdd on to a Pre-designed PanelDesign Fully Custom Panels
Single Cell Gene Expression
Single Cell Immune Profiling
Spatial Gene Expression


  1. 1Step 1

    Select Your Panel

    Decide what genes you want to focus on. Use one of our comprehensive, pre-designed panels with or without added genes, or design from scratch with the 10x Genomics Custom Panel Designer. The use of fully custom panels with Spatial Gene Expression is not supported at this time.

  2. 2Step 2

    Enrich Your 10x Library

    Start with an existing 10x Genomics single cell library or sequencing-ready Visium Gene Expression library from a tissue section. Perform hybrid capture with the selected gene panel to enrich for transcripts of interest.

  3. 3Step 3


    The resulting 10x Barcoded, target-enriched library is compatible with standard NGS short-read sequencing on Illumina sequencers for efficient transcriptional profiling of individual cells or tissue sections.

  4. 4Step 4

    Analyze Your Data

    Convert the raw sequencing data to biologically meaningful insights with targeted analysis pipelines in Cell Ranger or Space Ranger.

    Analysis pipelines output

    Output includes QC information and files that can be easily used for further analysis in our Loupe visualization software, or third-party R or Python tools.

  5. 5Step 5

    Visualize Your Data

    Use Loupe Browser visualization software to interactively explore your single cell or spatial results. Perform differential gene expression analysis between clusters and samples to identify cell types, distinguishing genes, and more.

    Do I need to be a bioinformatician to use it?

    Loupe is a point-and-click software that’s easy for anyone to download and use.


Frequently Asked Questions

When used in conjunction with 10x Genomics Single Cell Gene Expression workflows, it provides you with expression profiles of a set of targeted genes, from hundreds to thousands of single cells in suspension. When paired with Visium Spatial Gene Expression workflows, it provides you with histological and spatially resolved targeted gene expression profiles from an intact tissue section.

In general, a targeted approach can greatly increase the efficiency and decrease the cost of gene expression studies. Since you are focusing sequencing on a subset of relevant genes, you can reduce sequencing costs by up to 90% while maintaining the same sequencing depth.

Targeted gene expression for single cells is compatible with fresh and cryopreserved single cell suspensions. Pre-designed panels currently target human genes, but custom mouse panels can be designed. For Visium workflows, the assay is compatible with fresh frozen tissues containing mRNA. A list of tissues successfully tested in-house can be found here.

List of tissues successfully tested in-house

Add up to 200 genes to any pre-designed panel for single cell or spatial targeted gene expression with the Custom Panel Designer. For targeted single cell gene expression design fully custom panels from 10 to 1,500 genes.

For Chromium experiments, Cell Ranger is an analysis software that automatically generates expression profiles for each cell and identifies clusters of cells with similar expression profiles. You can then use Loupe Browser, a visualization software, to interactively explore the results. You can download Cell Ranger and Loupe Browser from the 10x Genomics support site at no cost.

For Visium experiments, Space Ranger is an analysis software that automatically generates expression profiles for each spot and identifies clusters of spots with similar expression profiles. You can then use Loupe Browser, a visualization software, to interactively explore results. You can download Space Ranger and Loupe Browser from the 10x Genomics support site at no cost.

Download software at 10x Support

Compatible Products


Single Cell Gene Expression

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Single Cell Immune Profiling

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Spatial Gene Expression

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  • 3' whole transcriptome gene expression
  • Sample multiplexing
  • Paired full-length TCR / BCR sequencing
  • 5’ whole transcriptome gene expression
  • 3' whole transcriptome gene expression
  • Compatible with FFPE and fresh frozen tissue sections


  • Cell Surface Protein
  • CRISPR Screening
  • Sample multiplexing
  • Cell Surface Protein
  • Antigen Specificity
  • CRISPR Screening
  • Immunofluorescence protein co-detection
  • Visium CytAssist Gene and Protein Expression


  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
Single Cell Gene Expression

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