Spatial Transcriptomics Sequencing

Combines next-generation sequencing with spatial information to uncover cellular heterogeneity and tissue architecture

Spatial transcriptomics enables the comprehensive characterization of gene expression within its native tissue context, providing unprecedented insights into cellular organization, tissue architecture, and cell–cell interactions.

Novogene offers end-to-end spatial transcriptomics solutions, from experimental design and sample processing to sequencing and advanced bioinformatics analysis. Powered by leading platforms including 10x Genomics Visium and STOmics Stereo-seq, our services deliver high-resolution spatial profiling to support discoveries in oncology, immunology, neuroscience, developmental biology, and precision medicine. Backed by extensive multi-omics expertise and dedicated scientific support, Novogene helps researchers transform complex spatial data into meaningful biological insights.

Spatial Transcriptomics Platforms at Novogene

10x Genomics Visium HD

High-resolution spatial gene expression profiling

Compatible with FFPE, fresh frozen, and fixed frozen samples

Improved gene detection sensitivity across spatial domains

10x Genomics Visium HD 3’

Broad eukaryotic species support

Optimized for poly-A transcript detection

Ideal for scalable spatial transcriptomics across diverse species

STOmics Stereo-seq OMNI FFPE

Ultra-high throughput spatial transcriptomics

Suitable for large tissue sections

Massive spatial capture area for whole-tissue profiling

Benefits of Novogene’s Spatial Transcriptomics Service

PhD-Level Expert Team

Novogene’s PhD-level scientists provide expertise in experimental design and bioinformatics. With 20+ years of pathology and tissue research experience, our team ensures reliable sample processing and accurate spatial data analysis.

Advanced Technology Platforms

We offer advanced spatial transcriptomics solutions, including Visium HD, Visium HD 3’, and Stereo-seq. State-of-the-art imaging and tissue-processing systems ensure high-quality spatial profiling and analysis.

Proven Experience Across Diverse Projects

Novogene has completed over 4,000 spatial and transcriptomics projects across 50+ species and 100+ tissue types, supporting diverse research areas with robust workflows and reproducible results.

High-Impact Scientific Outcomes

Novogene has contributed to 350+ publications in leading journals, including Nature and Cell. Our high-quality data and analytical expertise support impactful discoveries and successful publication outcomes.

Applications of Spatial Transcriptomics

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

Cancer Research

Explore the spatial architecture of tumors by mapping gene expression directly within tissue sections. This approach helps uncover interactions between cancer, immune, and stromal cells that influence disease progression and treatment outcomes.

Developmental Biology

Gain insight into how tissues and organs form by linking gene activity to precise anatomical locations. Spatially resolved data provide a powerful framework for studying development, differentiation, and morphogenesis.

Neuroscience

Investigate molecular patterns across brain regions and neural circuits while preserving tissue context. Spatial analysis enables a deeper understanding of brain organization, function, and neurological disorders.

Infectious Disease & Immune Response

Characterize where immune cells reside, interact, and become activated during infection or inflammation. These spatial insights help reveal mechanisms of host defense, tissue immunity, and disease pathogenesis.

Applications of Spatial Transcriptomics

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

Cancer Research

Developmental Biology

Neuroscience

Infectious Disease & Immune Response

Specifications

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Project Workflow

Specifications

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Project Workflow

Resources

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.

Service flyers

Novogene 10x Visium HD & Visium HD (3‘) Spatial Transcriptome Sequencing

Spatial transcriptomics is a revolutionary technology that can profile gene expression within tissue samples while preserving their natural spatial context. Unlike traditional transcriptomics, which analyzes gene expression in bulk, spatial transcriptomics enables detailed visualization of how genes are expressed across different regions and cells of a tissue or organ. This powerful tool has been widely applied in research across oncology, neuroscience, immunology, developmental biology, drug discovery,and more.

Webinars

Seeing is Believing: A Beginner’s Guide to Spatial Transcriptomics

This webinar will present the spatial transcriptomics service from the technology to application, from sample preparation to data analysis, helping you to understand how this powerful tool is applied to unlock the complex biological processes.

More Services

10x Single Cell RNA Sequencing

Illumina PIP-seq Single Cell 3’ RNA Sequencing

Whole transcriptome sequencing

mRNA Sequencing

Total RNA Sequencing

Metatranscriptome Sequencing

Isoform Sequencing (Full-length Transcrip Sequencing)

Ready to Start Your Project?

Our platform offers tailored solutions for

your unique experimental needs, ensuring a seamless experience from project design to data delivery.

Spatial Transcriptomics Sequencing

Combines next-generation sequencing with spatial information to uncover cellular heterogeneity and tissue architecture

Spatial Transcriptomics Platforms at Novogene

10x Genomics Visium HD

High-resolution spatial gene expression profiling

Compatible with FFPE, fresh frozen, and fixed frozen samples

Improved gene detection sensitivity across spatial domains

10x Genomics Visium HD 3’

Broad eukaryotic species support

Optimized for poly-A transcript detection

Ideal for scalable spatial transcriptomics across diverse species

STOmics Stereo-seq OMNI FFPE

Ultra-high throughput spatial transcriptomics

Suitable for large tissue sections

Massive spatial capture area for whole-tissue profiling

Benefits of Novogene’s Spatial Transcriptomics Service

PhD-Level Expert Team

Advanced Technology Platforms

Proven Experience Across Diverse Projects

Novogene has completed over 4,000 spatial and transcriptomics projects across 50+ species and 100+ tissue types, supporting diverse research areas with robust workflows and reproducible results.

High-Impact Scientific Outcomes

Applications of Spatial Transcriptomics

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

Cancer Research

Developmental Biology

Neuroscience

Infectious Disease & Immune Response

Applications of Spatial Transcriptomics

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

Cancer Research

Developmental Biology

Neuroscience

Infectious Disease & Immune Response

Specifications

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Project Workflow

Specifications

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sample Requirements

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

*FFPE glass slides must be positive charged glass slides.

Service	Sample Input Type
	FFPE Blocks	FFPE Slides	FF OCT Blocks
10x VIsium HD 3’	❌	❌	✅
10x VIsium HD	✅	✅	✅
Stereo-Seq OMNI FFPE	✅	✅	❌
Sample Requirement	1 block, placed in a plastic dehydration box	• RNA QC: 5-10 FFPE sections (10μm thickness), placed in a tube; • Library construction: 2-4 FFPE tissue sections (5μm thickness), placed on slides and stored in slide mailing boxes	Tissue thickness >1mm, area <6.5×6.5mm
Storage Conditions	4℃ storage after embedding, protected from light	Dry and sealed, 4℃ storage for no more than 30 days	-80℃ storage, mark the cutting surface on the embedding box
Shipping Conditions	4℃ or room temperature	4℃ or room temperature	Dry ice shipping

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Sequencing and Analysis

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

	10x Visium HD	10x Visium HD 3’	Stereo-Seq OMNI FFPE
Species	Human & Mouse	Broad Eukaryotes*
Resolution	2um		0.5-0.6um
Sequencing Platform	Illumina NovaSeq XPlus		DNB-Seq
Read Length	PE150		PE75
Recommended Data Amount	300M Read Pairs ~ 100Gb/sample	210Gb/sample	2.5B Reads/sample
Bioinformatics Analysis	• Data QC • Data mapping and gene expression quantification • Space Ranger/SAW analysis • Principal component analysis (PCA) • Clustering and dimensionality reduction analysis • Cluster marker gene detection • Spatial distribution of cluster marker genes • Functional enrichment analysis (GO/KEGG/Reactome pathway enrichment)

Project Workflow

Resources

Demo Results

1/1

Spatial quantification of gene expression in bins

1/1

Clustering analysis presentation: spatial distribution, tSNE and UMAP

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.

Service flyers

Novogene 10x Visium HD & Visium HD (3‘) Spatial Transcriptome Sequencing

Webinars

Seeing is Believing: A Beginner’s Guide to Spatial Transcriptomics

More Services

10x Single Cell RNA Sequencing

Illumina PIP-seq Single Cell 3’ RNA Sequencing

Whole transcriptome sequencing

mRNA Sequencing

Total RNA Sequencing

Metatranscriptome Sequencing

Isoform Sequencing (Full-length Transcrip Sequencing)

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