Visium HD Spatial Gene Expression

Novogene’s spatial transcriptomics service is powered by the 10X Genomics’ Visium HD WT Panel Gene Expression, which delivers whole transcriptome spatial gene expression at single-cell resolution. Compatible with both fresh frozen (OCT embedded) and FFPE tissues, it preserves morphology through histological imaging and transfers capture probes with CytAssist to ensure accurate spatial barcoding, enabling researchers to visualize gene expression within intact tissue architecture and uncover complex cellular interactions.

With no gaps in tissue coverage and 6.5 x 6.5 mm dual capture areas per slide, this new platform brings your FFPE tissue analysis into ultra-high definition. This probe-based gene expression profiling technology from 10X Genomics is designed specifically for FFPE samples and targets approximately 18,000 genes in humans and 20,000 genes in mice, providing information on the whole transcriptome. Novogene also utilizes the 10X Visium CytAssist platform for facilitating the transfer of the transcriptomic probes from the glass slide to a capture area on the Visium slide, thus minimizing mislocalization and maintaining spatiality.

Why Choose Novogene for Spatial Gene Expression Sequencing?

End-to-End Service

Complete workflow from sample QC to NovaSeq X Plus sequencing and publication-ready outputs

High-Quality Data

Industry-standard, high-quality sequencing data enabling reliable downstream bioinformatics analysis

Comprehensive Bioinformatics Support

Space Ranger and Seurat-based analysis with publication-ready figures for spatial insights

Extensive Experience

Proven experience across diverse human and mouse tissues for spatial profiling applications

Customer Service System

Online portal for project tracking, data access, reporting, and efficient team collaboration

Applications of Spatial Transcriptomics

Spatial transcriptomics has been assisting researchers in the following research areas, including:

Cancer research

Visium HD helps visualize how different cell types—like tumor, immune, and stromal cells—are organized in a tumor, revealing spatial patterns that impact progression and treatment response.

Developmental biology

Visium HD provides high-resolution, multidimensional spatial profiling data for developmental biology research, promoting a deeper understanding of embryonic development, organ formation, and cell fate regulation mechanisms. It also supports applications such as precision breeding and disease model construction.

Neuroscience

High-resolution mapping of gene expression is possible across brain regions and layers, helping researchers study brain function, development, and neurological diseases like Alzheimer's.

Infectious Disease & Immune Response

Visium HD can reveal how immune cells are distributed and activated in tissues during infection, offering insights into host-pathogen interactions and inflammation.

Applications of Spatial Transcriptomics

Spatial transcriptomics has been assisting researchers in the following research areas, including:

Cancer research

Visium HD helps visualize how different cell types—like tumor, immune, and stromal cells—are organized in a tumor, revealing spatial patterns that impact progression and treatment response.

Developmental biology

Neuroscience

High-resolution mapping of gene expression is possible across brain regions and layers, helping researchers study brain function, development, and neurological diseases like Alzheimer's.

Infectious Disease & Immune Response

Visium HD can reveal how immune cells are distributed and activated in tissues during infection, offering insights into host-pathogen interactions and inflammation.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE slide**	5-10 FFPE (10μm thickness) scrolls in tube for sample QC; 2-4 FFPE (5μm thickness) tissuesections on glass slides, for library prep*	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	Tissue thickness > 1mm FFPE blocks should be no older than 3 years *FFPE glass slides must be positive charged glass slides	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

	Visium HD
Species	Human or mouse
Resolution	2 μm (single cell level)
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	FFPE: 100 Gb/sample; Fresh Frozen: 210 Gb/sample
Analysis	Data QC: Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Project Workflow

Demo Results

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Spatial Quantification of Gene Expression in Bins

Space Ranger is used to count the UMI for each gene on every bin, obtaining a bin-gene expression matrix for the sample. After performing data QC, the figure below shows the distribution of UMI per gene across the spatial regions of the tissue.

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Clustering Analysis Presentation: Spatial Distribution, tSNE and UMAP

Cluster_Spatial: spatial distribution map of clusters; Cluster_tSNE: tSNE two-dimensional spatial representation map of clusters; Cluster_UMAP: UMAP two-dimensional spatial representation map of clusters

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t-SNE and UMAP Dimensionality Reduction of Differentially Expressed Genes

The top 4 differentially expressed genes of each cluster are displayed in several ways. The figure presents the t-SNE and UMAP dimensional reduction visualization of differentially expressed genes.

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Visium HD Spatial Gene Expression