HD 3’ Gene Expression
Recommended Visium assay for expanded spatial discovery applications
Single cell-scale resolution
Why choose HD 3' Gene Expression
Diverse species compatibility for fresh frozen tissue samples
De novo discovery, including feasibility for isoform, BCR/TCR, and SNV detection
Assay specifications
Agnostic
Species
Fresh frozen tissue
Compatible samples
3' Gene expression
Morphology (H&E)
Isoform expression (feasibility)
TCR & BCR sequencing (feasibility)
Multiomics
Compatible instruments
Throughput options
Capture Area size: 6.5 x 6.5 mm
Assay components
Consumables
Index Kit
1000215
Dual Index Kit TT Set A, 96 rxn
Core Slides and Reagents
1000857
Visium HD 3', 6.5 mm, 4 rxns
1000856
Visium HD 3', 6.5 mm, 16 rxns
1000854
Visium HD 3' Reagents - Kit A Small
Starter Kits and Accessories
1000857
Visium HD 3', 6.5 mm, 4 rxns
Optional Accessories
1000499
Visium CytAssist Reagent Accessory Kit
1000886
Visium CytAssist Alignment Aid Kit, 6.5 mm
Documents and resources
User guides
Sample prep
Technical notes
Sequencing requirements
The final gene expression library is sequenced at a recommended minimum depth of 550 million read pairs for Capture Areas fully covered by tissue.
Resources
Deeper spatial exploration with Visium HD 3'
Getting started with Visium HD data analysis and third-party tools
Data analysis
Space Ranger Analysis Pipelines
Free analysis pipelines that process the input file types to align Visium sequencing data with the tissue image and perform optional cell segmentation.
Loupe Browser
Desktop application for Windows and MacOS that allows you to interactively visualize data.
Cloud Analysis
Cloud Analysis enables quick and easy access to Cell Ranger pipelines from your web browser.
Featured datasets
Related products
Visium HD WT Panel
Probe-based spatial gene expression assay for comprehensive differential gene expression at single cell scale.
Visium v2 WT Panel
Probe-based spatial gene expression assay utilizing first-generation slide architecture with a large Capture Area option.
Visium v1 3'
3' poly(A) capture-based spatial gene expression assay utilizing first-generation slide architecture. Upgrading to HD 3' is recommended.