Stereo-Seq Spatial Gene Expression

STOmics’ flagship technology, Spatial Enhanced Resolution Omics-sequencing (Stereo-seq), is an advanced spatial transcriptomics platform based on DNA Nano Ball (DNB) technology. This cutting-edge system offers unparalleled resolution, throughput, and field of view, enabling comprehensive spatial transcriptomic analysis across multiple scales — tissue, cellular, subcellular, and molecular levels. Using a patterned array chip and Coordinate ID (CID) system, Stereo-seq captures mRNA directly from tissue samples, restoring its precise spatial coordinates. As a transformative tool, Stereo-seq empowers researchers to elucidate the complex relationships between gene expression, cell morphology, and their local microenvironments.

Why Choose Novogene for Stereo-Seq Spatial Gene Expression Sequencing?

Large Area High Resolution

500 nm resolution with up to 13 cm × 13 cm capture area for gene and imaging analysis

Broad Sample Compatibility

Compatible with fresh-frozen and FFPE samples across diverse animal and plant tissue types

Pathology Integration

Single-section staining enables simultaneous pathological assessment and spatial transcriptomics analysis

Applications of Stereo-Seq Spatial Gene Expression

Unlock comprehensive insights into human genetics for hereditary disease, cancer, and population studies.

Tumor Microenvironment Research

Characterize the molecular and cellular landscape of the tumor microenvironment.

Immunology

Map the spatial distribution and interactions of immune cells within tissues.

Neuroscience

Investigate neural cell function and expression patterns at unprecedented resolution.

Biomarker Discovery

Identify cell-specific biomarkers for disease diagnosis and therapy development.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

Sequencing and Analysis

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

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

Sequencing and Analysis

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

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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

1/1

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.

1/1

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

1/1

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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Stereo-Seq Spatial Gene Expression

Why Choose Novogene for Stereo-Seq Spatial Gene Expression Sequencing?

Large Area High Resolution

500 nm resolution with up to 13 cm × 13 cm capture area for gene and imaging analysis

Broad Sample Compatibility

Compatible with fresh-frozen and FFPE samples across diverse animal and plant tissue types

Pathology Integration

Single-section staining enables simultaneous pathological assessment and spatial transcriptomics analysis

Applications of Stereo-Seq Spatial Gene Expression

Unlock comprehensive insights into human genetics for hereditary disease, cancer, and population studies.

Tumor Microenvironment Research

Characterize the molecular and cellular landscape of the tumor microenvironment.

Immunology

Map the spatial distribution and interactions of immune cells within tissues.

Neuroscience

Investigate neural cell function and expression patterns at unprecedented resolution.

Biomarker Discovery

Identify cell-specific biomarkers for disease diagnosis and therapy development.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

Sequencing and Analysis

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

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

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 sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

Sequencing and Analysis

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

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/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

1/1

Spatial Quantification of Gene Expression in Bins

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Clustering Analysis Presentation: Spatial Distribution, tSNE and UMAP

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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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