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.

Targeted Gene Expression
  • More for less

    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

    Increase flexibility

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

  • Stay on target

    Stay on target

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

  • Seamless integration

    Seamless integration

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

  • Built to scale

    Built to scale

    Easily scale sample throughput by multiplexing libraries during target enrichment.

  • Streamlined data analysis

    Streamlined data analysis

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

What You Can Do

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
Coming soon: Human Neuroscience Panel

    Add on to Pre-designed Panels

    Customize pre-designed panels and add up to 200 additional genes with the 10x Genomics Custom Panel Designer. Or, if you already have a specific set of genes you want to analyze, you can create those panel designs from scratch.

    Create Fully Custom Panels

    If you’d like to start from scratch and tackle a different research area altogether, or you have a specific set of 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

    Create an account

    Design custom panels and save them to your account.

    Select your panel type

    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

    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

    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.


    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.

    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. Fixed panels currently target human genes. 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.

    The pre-designed panels offered by 10x Genomics are comprehensive, with over 1,000 genes in each panel. Add up to 200 genes with the Custom Panel Designer, or 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 Support site at no cost. For Visium experiments, a supported protocol along with software analysis for targeted panels will be coming Fall 2020.

    Compatible Products

    Single Cell Gene Expression

    Single Cell Immune Profiling

    Spatial Gene Expression

    • 3’ transcriptome gene expression in tissues
    • Targeted gene expression
    • Paired full-length TCR / BCR sequencing
    • 5’ whole transcriptome gene expression
    • Targeted gene expression
    • 3’ transcriptome gene expression in tissues
    • Cell Surface Protein
    • CRISPR Screening
    • Cell Surface Protein
    • Antigen Specificity
    • Immunofluorescence Protein Co-detection

    * Optimized protocol, support, and software for targeted panels with spatial gene expression coming Fall 2020

    Single Cell Gene Expression

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