10X Single Cell Immune Profiling Services

Single-cell Immune Profiling

Single-cell analysis of immune repertoires and transcriptional states to explore immune diversity, clonality and functional phenotypes.

Single-cell immune profiling combines 5′ gene expression analysis with V(D)J sequencing of T cell receptors (TCRs) and B cell receptors (BCRs) to study immune cell identity, activation state and clonal diversity at single-cell resolution. This approach helps connect what immune cells are expressing with their receptor sequences, supporting a more complete view of immune function and repertoire diversity.

Novogene Europe supports immune profiling studies using 10x Genomics Universal 5' Gene expression assay. The service can help researchers characterise T and B cell populations, investigate clonal expansion, compare immune repertoires across samples or conditions, and explore transcriptional changes linked to disease models, treatment response or immune activation.

Service Highlights

5′ Gene Expression & Immune Repertoire Profiling

Combine single-cell 5′ gene expression analysis with TCR and BCR sequencing to connect immune cell transcriptional states with receptor clonotypes.

TCR and BCR Clonotype Analysis

Characterise immune repertoire diversity, clonal expansion and receptor usage across samples, helping link T and B cell clonotypes with immune response patterns.

10x Genomics Chromium iX Workflow

Library preparation using 10x Genomics Chromium iX technology and GEM-X chemistry to support high-resolution immune profiling at single-cell level.

Integrated Bioinformatics Analysis

Analysis outputs can include gene expression clustering, cell-type annotation, clonotype statistics, CDR3 analysis, V/J gene usage and clonal diversity assessment.

Applications

Immune Repertoire Analysis

Characterise TCR and BCR diversity, receptor usage and clonotype distribution across samples, cohorts or experimental conditions to explore immune repertoire structure.

Clonal Expansion and Response

Identify expanded T or B cell clonotypes and examine how immune populations respond to disease, treatment, vaccination or immune stimulation.

Tumour and Tissue Immunology

Study immune cell composition, activation states and clonal patterns within complex tissue environments, including tumour or inflammatory samples.

Autoimmune and Infectious Disease Research

Investigate immune population changes, repertoire features and transcriptional response patterns linked to infection, autoimmunity or immune-mediated disease.

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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity Analysis

Resources

Example Analysis Output

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CDR3 Length Profile

Review CDR3 length patterns to support repertoire characterisation and sample comparison.

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Clonotype Count

Compare the number of unique clonotypes across samples or groups to explore immune repertoire diversity.

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V Gene Usage

Visualise V gene usage patterns across samples to identify receptor usage differences within the T cell repertoire.

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Clonal Proportion

Compare the proportion of expanded and low-frequency clonotypes to assess clonal structure across samples.

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V-J Gene Pairing

Visualise V-J gene pairing relationships to support interpretation of receptor recombination and repertoire diversity.

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 10x Genomics Immune Profiling sequencing?

10x Genomics Immune Profiling currently supports human and mouse samples.

The assay uses probes that specifically target human and mouse V(D)J genes, which limits its application to these two species.

Researchers should consult with us before starting a project to confirm suitability.

Which tissue types are suitable for 10x Genomics Immune Profiling sequencing?

What sample preservation methods are recommended for 10x Genomics Immune Profiling sequencing?

What information does 5′ GEX with immune profiling generate?

How does immune profiling differ from standard scRNA-seq?

Which immune receptors can be analyzed using this platform?

What sample types are suitable for 5′ immune profiling?

Does this approach support comparative studies across conditions or time points?

What bioinformatics outputs are provided?

Can immune profiling data be integrated with other single-cell or omics datasets?

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 Immune Profiling

Single-cell analysis of immune repertoires and transcriptional states to explore immune diversity, clonality and functional phenotypes.

Service Highlights

5′ Gene Expression & Immune Repertoire Profiling

Combine single-cell 5′ gene expression analysis with TCR and BCR sequencing to connect immune cell transcriptional states with receptor clonotypes.

TCR and BCR Clonotype Analysis

Characterise immune repertoire diversity, clonal expansion and receptor usage across samples, helping link T and B cell clonotypes with immune response patterns.

10x Genomics Chromium iX Workflow

Library preparation using 10x Genomics Chromium iX technology and GEM-X chemistry to support high-resolution immune profiling at single-cell level.

Integrated Bioinformatics Analysis

Analysis outputs can include gene expression clustering, cell-type annotation, clonotype statistics, CDR3 analysis, V/J gene usage and clonal diversity assessment.

Applications

Immune Repertoire Analysis

Characterise TCR and BCR diversity, receptor usage and clonotype distribution across samples, cohorts or experimental conditions to explore immune repertoire structure.

Clonal Expansion and Response

Identify expanded T or B cell clonotypes and examine how immune populations respond to disease, treatment, vaccination or immune stimulation.

Tumour and Tissue Immunology

Study immune cell composition, activation states and clonal patterns within complex tissue environments, including tumour or inflammatory samples.

Autoimmune and Infectious Disease Research

Investigate immune population changes, repertoire features and transcriptional response patterns linked to infection, autoimmunity or immune-mediated disease.

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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Species*	Sample Type**	Sample Amount	Transportation Method
scRNA-seq	Human Mouse	Fresh cell suspension	Recommended Amount:300,000 cells per sample; (minimum ≥ 100,000 cells)	Needs to be shipped with ice packs
scRNA-seq	Human Mouse	Fresh tissue	Tissue weight ≥ 200mg (minimum ≥ 100mg) ≥ 2 tissue pieces/sample, separate 1.5ml cryovials	Needs to be shipped with ice packs within 48hrs of harvest

*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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity 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	Minimum 20,000 read pairs/cell for gene expression; 5,000 read pairs/cell for V(D)J
Analysis	Cell Ranger Analysis(gene expression)	Standard Analysis(gene expression)	Standard Analysis(V(D)J)
	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.	Demultiplex BCL files from a sequencer into FASTQs. Construction of Immune Repertoire(Alignment,Assembling contigs,Annotating contigs, Cell identification,Generating clonotype) Cell Filtration Clonotypes Statistics CDR3 Length Statistics Display of VJ Gene Abundance for Each Sample Clonotypes for Displaying VJ Gene Combinations Analysis of Highly Expressed Clonotypes by Multi-Sample Comparison Clone Proportion Analysis Clonal Diversity Analysis

Resources

Example Analysis Output

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CDR3 Length Profile

Review CDR3 length patterns to support repertoire characterisation and sample comparison.

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Clonotype Count

Compare the number of unique clonotypes across samples or groups to explore immune repertoire diversity.

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V Gene Usage

Visualise V gene usage patterns across samples to identify receptor usage differences within the T cell repertoire.

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Clonal Proportion

Compare the proportion of expanded and low-frequency clonotypes to assess clonal structure across samples.

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V-J Gene Pairing

Visualise V-J gene pairing relationships to support interpretation of receptor recombination and repertoire diversity.

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Frequently Asked Questions

What species are suitable for 10x Genomics Immune Profiling sequencing?

10x Genomics Immune Profiling currently supports human and mouse samples.

The assay uses probes that specifically target human and mouse V(D)J genes, which limits its application to these two species.

Researchers should consult with us before starting a project to confirm suitability.

Which tissue types are suitable for 10x Genomics Immune Profiling sequencing?

What sample preservation methods are recommended for 10x Genomics Immune Profiling sequencing?

What information does 5′ GEX with immune profiling generate?

How does immune profiling differ from standard scRNA-seq?

Which immune receptors can be analyzed using this platform?

What sample types are suitable for 5′ immune profiling?

Does this approach support comparative studies across conditions or time points?

What bioinformatics outputs are provided?

Can immune profiling data be integrated with other single-cell or omics datasets?

Explore Single-cell & Spatial Resources

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

Speak with a Specialist

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