10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger5.0, printed on 12/03/2024

Targeted Gene Expression Overview

Targeted Gene Expression technology focuses on a selected panel of relevant targeted genes which are directly enriched from a Chromium single-cell RNA-seq library prior to sequencing. Specific enrichment of the targeted molecules of interest by hybridization-capture enables Targeted Gene Expression to provide enhanced information about the expression of targeted genes at significantly lower sequencing depths. Targeted Gene Expression is fully compatible with both the Chromium single-cell 3’ gene expression and 5’ gene expression solutions (including Feature Barcode Technology), and relies on the same underlying Cell Ranger analysis software.

Resources and additional information are available below:

• For background information on Targeted Gene Expression see the Targeted Gene Expression Glossary
• To learn how to use Cell Ranger with Targeted Gene Expression data see Targeted Gene Expression Analysis
• For more information on the pre-designed gene panels available for Targeted Gene Expression see Pre-Designed Panels for Targeted Gene Expression
• To generate a new customized target gene panel for Targeted Gene Expression see the 10x Genomics Custom Panel Designer
• To learn how to compare targeted data with its parent whole transcriptome data see the targeted-compare pipeline
• To learn how to estimate recommended sequencing depths for targeted data from an existing whole transcriptome analysis dataset see the new Cell Ranger command targeted-depth