10xgenomics.com/products/targeted-gene-expression

Product Sheet10x Genomics | Chromium and Visium | Targeted Gene Expression

A targeted approach to single cell and spatial gene expression

Targeted Gene ExpressionTarget all the relevant genes and biomarkers to gain a com-plete view of the biology most important to your research with Targeted Gene Expression from 10x Genomics. Scale up your studies by increasing sample throughput while reducing sequencing costs, or measure all relevant genes at once with comprehensive and curated gene panels.

Compatible with Chromium Single Cell Gene Expression and Chromium Single Cell Immune Profiling, as well as Visium Spatial Gene Expression, you can profile a defined set of transcripts with pre-designed cancer, immunology, gene signature, and neuroscience panels or design your own custom content. While whole transcriptome analysis is key for early discovery, targeting the most relevant cell types and biomarkers lets you accelerate your validation studies into actionable insights.

Figure 1. Targeted Gene Expression provides flexibility and efficiency to scale any research project. Targeted Gene Expression enables the enrichment and analysis of a targeted set of mRNAs and is compatible with Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcode technology, and Spatial Gene Expression. Targeted gene panels are fully customizable. Choose one of our comprehensive and validated panels of over 1,000 genes, or design your own panel from scratch.*

Highlights • Get started faster by using comprehensive,

pre-designed panels with the ability to add up to 200 genes

• Focus on the genes most relevant to your research by designing a fully custom panel* with our Custom Panel Designer

• Increase sequencing efficiency with higher throughput and up to 90% lower cost

• Streamline your workflow while maintaining high gene sensitivities and reducing computa-tional burden

• Transition seamlessly between whole tran-scriptome and targeted analysis from the same library preparation to validate discover-ies or explore new hypotheses

Compatible library typesTargeted Gene Expression panels

Human Pan-Cancer Panel: 1,253 genes

Human Immunology Panel: 1,056 genes

Human Gene Signature Panel: 1,142 genes

Human Neuroscience Panel: 1,186 genes

Custom Human or Mouse Panels:* 10–1,500 user-defined genes

Add up to 200 genes to pre-designed panels with the Custom Panel DesignerSingle Cell Gene Expression with CRISPR screening & cell surface protein expression

Single Cell Immune Profiling with antigen specificity & cell surface protein expression

Spatial Gene Expression with immunofluorescenceprotein detection

*Targeted Spatial Gene Expression with fully custom panels is not supported at this time.

2 10xgenomics.com/products/targeted-gene-expression

A targeted approach to single cell and spatial gene expression

Product features• Go from cells or tissue section to enriched library

with an end-to-end workflow that takes as little as two days, letting you spend more time analyzing data and making discoveries

• Measure both gene and cell surface protein expression or CRISPR perturbations in single cells by combining Targeted Gene Expression with our Feature Barcode technology, meaning you won't miss out on multiomic readouts while reducing the sequencing costs for gene expression profiling

• Simultaneously assess TCR, Ig, and 5’ gene expression in the same cell by combining Tar-geted Gene Expression with Single Cell Immune Profiling, enabling immune receptor mapping and immunophenotyping at scale

• Visualize relevant gene and protein expression in the same tissue section by combining Targeted Spatial Gene Expression with immunofluorescence, providing co-localization of gene and protein expression for all your genes of interest at once

• Work with your preferred tissue type. Targeting is compatible with most human and mouse cell lines, primary cells, and dissociated tissue, as well as fresh frozen human tissue sections

• Minimize the introduction of bias by leveraging a hybrid capture approach to library enrichment

Figure 2. Streamlined workflow for Targeted Gene Expression helps accelerate your research. Starting with a final, barcoded library from Chro-mium Single Cell Gene Expression, Chromium Single Cell Immune Profiling, or Visium Spatial Gene Expression, up to eight input libraries can be pooled before target enrichment using hybrid capture. Enriched libraries can be sequenced at up to 90% lower cost than that of a corresponding whole tran-scriptome library and then analyzed with Cell Ranger or Space Ranger, our analysis pipelines that take your list of target genes and sequencing results as input. Visualization of data from targeted libraries and comparison of targeted and whole transcriptome libraries can be performed with Loupe Browser, our easy-to-use visualization software for single cell or spatial data.

Targetenrichment

Inputsample

Single Cell/SpatialGene Expression

Librarypooling

Targeted librarysequencing

Data analysis andvisualization

Single cell suspension

Tissue section

H&E or Immunofluorescence

310x Genomics

Product Sheet

Figure 3. Targeted Gene Expression preserves cell-type clustering and annotation of single cell data. Representative data from 6,000 human PBMCs from a healthy donor transcriptionally profiled using Single Cell Gene Expression. A. Cell clustering and manual cell type annotation based on capture of mRNA from the whole transcriptome, sequenced at 100,000 reads per cell. B. The same library underwent target enrichment using the 10x Genomics Human Immunology Panel and was sequenced and subsampled to 2,000 reads per cell. All major cell subpopulations were preserved compared to the whole transcriptome parent sample.

Figure 4. Curated content refines spatial gene expression analysis. A human breast cancer tissue section was H&E stained and processed using the Visium Spatial Gene Expression workflow, then enriched for genes of interest using Targeted Gene Expression with the Human Pan-Cancer Panel. Shown are the H&E image (A), H&E image overlaid with total UMI counts for 196 genes from the breast cancer gene category of the Human Pan-Cancer Panel (B), and H&E image overlaid with ESR1 expression level (C).

A.

H&E

B.

H&E with breastcancer genes

Sum of total UMI counts Breast Cancer

10.0

0.0

C.

H&E with ESR1expression

ESR1 expression

7.0

0.0

A. B.

Whole transcriptome Targeted

25

0

–25

–50t-SNE1

t-SN

E2

–25 0 25

Cell–type calledBDendriticMonocytes_CD14Monocytes_CD16NKT_DoubleNegTc_E�ectorTc_MemoryTc_NaiveTh_MemoryTh_NaiveUndetermined

Cell type called25

0

–25

–50t-SNE1

t-SN

E2

–25 0 25

Cell–type calledBDendriticMonocytes_CD14Monocytes_CD16NKT_DoubleNegTc_E�ectorTc_MemoryTc_NaiveTh_MemoryTh_NaiveUndetermined

Cell type called

Product Sheet

Contact us 10xgenomics.com | info@10xgenomics.com © 2021 10x Genomics, Inc. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.LIT000080 - Rev G - Product Sheet - A targeted approach to single cell and spatial gene expression

A targeted approach to single cell and spatial gene expression

Products Product code

Target Hybridization Kit, 16 rxns 1000248

Library Amplification Kit, 16 rxns 1000249

Human Pan-Cancer Panel, 4 rxns 1000260

Human Pan-Cancer Panel, 16 rxns 1000247

Human Immunology Panel, 4 rxns 1000259

Human Immunology Panel, 16 rxns 1000246

Human Gene Signature Panel, 4 rxns 1000258

Human Gene Signature Panel, 16 rxns 1000245

Human Neuroscience Panel, 4 rxns 1000277

Human Neuroscience Panel, 16 rxns 1000278

Custom Panel Designer* bit.ly/10xgenomics-custom-designer

Visit Designer

Compatible products

Chromium Single Cell Gene Expression 10xgenomics.com/single-cell

Learn More

Chromium Single Cell Immune Profiling 10xgenomics.com/vdj

Learn More

Visium Spatial Gene Expression* 10xgenomics.com/spatial-gene-expression

Learn More

*Targeted Spatial Gene Expression with fully custom panels is not supported at this time.