10X Single Cell RNA Sequencing

Single-cell Gene Expression

High-resolution single-cell and single-nucleus transcriptome profiling to explore cellular heterogeneity, cell states and gene expression dynamics.

Single-cell gene expression analysis enables researchers to profile transcriptomes at individual cell resolution, helping to reveal cell types, functional states and cellular responses that may be missed by bulk RNA sequencing. It is widely used to study complex tissues, immune populations, developmental systems and disease-associated cellular heterogeneity.

Novogene Europe supports single-cell and single-nucleus 3′ gene expression studies using 10x Genomics GEM-X technology, with GEM-X workflows available for suitable projects. The service generates cell-level transcriptome profiles for downstream analysis, including quality assessment, clustering, marker gene identification, cell-type annotation and differential expression analysis.

Service Highlights

Single-cell and Single-nucleus Workflows

Support for both single-cell and single-nucleus gene expression analysis, helping researchers profile cell populations from complex tissues, fragile cell types and samples where whole-cell dissociation may be challenging.

Flexible Sample Compatibility

Workflow options support a range of sample types, including cryopreserved cells, fresh tissues, organoids, whole blood, bone marrow and fresh frozen tissue for nuclei-based analysis, depending on project design and sample suitability.

10x Genomics Chromium iX Workflow

Library preparation using 10x Genomics Chromium iX technology and GEM-X chemistry to generate high-resolution 3′ gene expression profiles at individual cell or nucleus level.

Cell-level Transcriptome Analysis

Analysis outputs include quality assessment, clustering, marker gene identification, cluster summaries and differential expression analysis for interpreting cellular heterogeneity.

Applications

Cell Population Mapping

Identify and compare cell populations within complex tissues, organoids, model systems or clinical research samples, including rare or previously uncharacterised cell types.

Cell State and Response Analysis

Investigate how cells change across conditions, treatments, disease models or time points by profiling transcriptional states and response-associated gene expression.

Tissue and Microenvironment Studies

Explore cellular composition and transcriptional changes within complex tissue environments, including tumour, immune, stromal, epithelial, neuronal or inflammatory compartments.

Development and Differentiation

Study dynamic gene expression patterns linked to cell differentiation, lineage progression and developmental processes across tissues, organoids or experimental models.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Resources

Example Analysis Output

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UMAP Clustering

Compare the relative abundance of annotated cell types across samples or study groups.

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Cell Type Composition

Compare the relative abundance of annotated cell types across samples or study groups.

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Cell State Potential

Assess predicted cell-state patterns to support interpretation of cellular transitions and functional heterogeneity.

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Cell-type t-SNE

Display annotated cell populations using t-SNE visualisation to support cell-type identification and exploratory analysis.

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Marker Gene Enrichment

Identify enriched pathways or functional categories associated with marker genes from selected cell clusters.

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Marker Gene Expression

Visualise marker gene expression across cell groups to support cluster annotation and biological interpretation.

Webinars

Unravel biological complexity with streamlined single cell solution

Discover how single-cell sequencing can reveal cellular heterogeneity, identify rare cell populations, and uncover molecular mechanisms within complex tissues. This webinar will explore 10x Genomics Chromium Single Cell solutions, key research applications, and best practices for generating and analysing high-quality single-cell data.

Learn More

Frequently Asked Questions

What species are suitable for the 10x Genomics 3' Single-Cell Transcriptome technology?‌

The beads on the 10x platform have a poly-dT structure that binds to the poly-A tail at the 3' end of mRNA molecules, enabling the capture of each individual mRNA molecule. Therefore, this platform is suitable for species whose mRNA molecules contain poly(A) tails (Note: Some mitochondrial or chloroplast genes in eukaryotes may not have poly-A tails and might not be detected). For downstream data analysis, a high-quality assembled and annotated reference genome is also recommended.

Which tissue types are suitable for 10x Genomics 3' Single-Cell Transcriptome?‌

What sample preservation methods are recommended for 3' Single-Cell Transcriptome?

What are the methods for preparing a single-cell suspension from fresh tissue?‌

Which tissue types are suitable for Single-Nucleus Transcriptome?‌

Explore Single-cell & Spatial Resources

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

Have a project in mind?

Send us your enquiry and a Novogene Europe specialist will be in touch.

Single-cell Gene Expression

High-resolution single-cell and single-nucleus transcriptome profiling to explore cellular heterogeneity, cell states and gene expression dynamics.

Service Highlights

Single-cell and Single-nucleus Workflows

Flexible Sample Compatibility

10x Genomics Chromium iX Workflow

Library preparation using 10x Genomics Chromium iX technology and GEM-X chemistry to generate high-resolution 3′ gene expression profiles at individual cell or nucleus level.

Cell-level Transcriptome Analysis

Analysis outputs include quality assessment, clustering, marker gene identification, cluster summaries and differential expression analysis for interpreting cellular heterogeneity.

Applications

Cell Population Mapping

Identify and compare cell populations within complex tissues, organoids, model systems or clinical research samples, including rare or previously uncharacterised cell types.

Cell State and Response Analysis

Investigate how cells change across conditions, treatments, disease models or time points by profiling transcriptional states and response-associated gene expression.

Tissue and Microenvironment Studies

Explore cellular composition and transcriptional changes within complex tissue environments, including tumour, immune, stromal, epithelial, neuronal or inflammatory compartments.

Development and Differentiation

Study dynamic gene expression patterns linked to cell differentiation, lineage progression and developmental processes across tissues, organoids or experimental models.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Service	Assay	Sample Type**	Recommended Amount	Other details
scRNA-seq	3’ GEX 5’ GEX + VDJ* (*Mouse and human only)	Cryopreserved cell suspension	2-3 M cells Cell viability > 70%	• Samples should be cryopreserved with freezing media. • Shipped in cryovials with dry ice.
		Fresh tissues/organoids	> 50 mg	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs.
		Whole blood/Bone marrow (Mouse, Human, Rat)	2-4 mL	• Novogene will ship tissue storage solution. • Tissues must be placed in tissue storage solution immediately after retrieval and arrive in the lab within 48 hours. • Shipped with ice packs. Whole blood/Bone marrow (Mouse, Human, Rat) 2-4 mL • Collected in EDTA vacutainer tubes. • Shipped with ice packs.
snRNA-seq	3’ GEX	Fresh Frozen tissues/organoids	> 50 mg	• Shipped in cryovials with dry ice.

*Contact us for species-specific recommendations and tissue type guidance.
**Sample type preferences may vary based on sequencing requirements and sample compatibility.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Sequencing Platform	Illumina NovaSeq X-Plus Sequencing Platform
Read Length	Paired-end 150 bp
Recommended Data	20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis	Cell Ranger Analysis	Standard Analysis
	Demultiplex BCL files from a sequencer into FASTQs. Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.). Alignment of reads to genome. Gene expression quantification. Clustering analysis. Differentially expression analysis between clusters. Visualization.	Demultiplex BCL files from a sequencer into FASTQs. Alignment, UMI counting, Metrics summary. Identification of highly variable gene (HVGs). Cell Subpopulation Identification. Principal component analysis (PCA). Identify clusters of cells. Dimensionality reduction and Visualization. Marker gene detection (Differentially expression analysis between clusters). GO/KEGG/Reactome Enrichment. FunctionalAnnotation of Transcription Factor. Protein-Protein Interaction Network Analysis.

Resources

Example Analysis Output

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UMAP Clustering

Compare the relative abundance of annotated cell types across samples or study groups.

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Cell Type Composition

Compare the relative abundance of annotated cell types across samples or study groups.

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Cell State Potential

Assess predicted cell-state patterns to support interpretation of cellular transitions and functional heterogeneity.

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Cell-type t-SNE

Display annotated cell populations using t-SNE visualisation to support cell-type identification and exploratory analysis.

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Marker Gene Enrichment

Identify enriched pathways or functional categories associated with marker genes from selected cell clusters.

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Marker Gene Expression

Visualise marker gene expression across cell groups to support cluster annotation and biological interpretation.

Webinars

Unravel biological complexity with streamlined single cell solution

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Frequently Asked Questions

What species are suitable for the 10x Genomics 3' Single-Cell Transcriptome technology?‌

Which tissue types are suitable for 10x Genomics 3' Single-Cell Transcriptome?‌

What sample preservation methods are recommended for 3' Single-Cell Transcriptome?

What are the methods for preparing a single-cell suspension from fresh tissue?‌

Which tissue types are suitable for Single-Nucleus Transcriptome?‌

Explore Single-cell & Spatial Resources

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

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Send us your enquiry and a Novogene Europe specialist will be in touch.