Single-Cell Immune Repertoire Sequencing
What Is Single-Cell Immune Repertoire Sequencing?
Single-cell immune repertoire sequencing is an advanced next-generation sequencing (NGS) approach that simultaneously analyzes immune receptor diversity (T-cell receptor [TCR] and B-cell receptor [BCR] sequences) and gene expression profiles from individual immune cells. This dual analysis provides an unprecedented level of resolution compared to bulk sequencing, which only measures average properties across mixed cell populations.
Each cell is encapsulated and barcoded, allowing its V(D)J receptor sequences to be paired with its transcriptome. This enables researchers to not only track clonal expansion and lineage relationships but also understand the phenotype, activation status, and functional state of every cell within the immune repertoire.
Key biological insights gained from this method include:
-
Precise clonal tracking: Follow how specific immune clones expand, contract, and evolve during disease progression or therapy.
-
Antigen-specific cell identification: Detect rare antigen-reactive T and B cells and analyze their transcriptional programs.
-
Immune state characterization: Classify cells into functional states (e.g., exhausted, activated, memory) based on gene expression signatures.
-
Integration with tissue context: Map immune diversity within complex microenvironments such as tumors or lymphoid tissues.
Because it captures both receptor specificity and cellular phenotype at once, single-cell immune repertoire sequencing is essential for understanding the complexity of adaptive immune responses in health, disease, and therapeutic interventions. This high-resolution data has become a cornerstone for studies in oncology, infectious disease, vaccine development, and autoimmunity, driving discoveries that are shaping the future of precision medicine.
Advantages of Single-Cell Immune Repertoire Sequencing
01
Integrated Receptor–Transcriptome Profiling: Captures both immune receptor sequences and full gene expression from the same single cell.
02
High-Resolution Clonal Tracking: Links clonal identity to cell states, enabling precise mapping of immune dynamics.
03
Phenotype–Function Insights: Reveals how transcriptional programs shape immune cell activity in health and disease.
04
Multi-Omic Capability: Compatible with additional modalities such as cell surface protein (CITE-seq) or epigenetic profiling.
05
Broad Sample Support: Works with fresh or cryopreserved single-cell suspensions from PBMCs, tumor tissue, or lymphoid organs.
06
Rare Clone Detection: Identifies low-frequency antigen-specific T/B cells by combining receptor data with phenotypic markers.
07
Cross-Species Flexibility: Supports human, mouse, and other preclinical models for translational research.
08
Expert Data Analysis: Includes advanced bioinformatics for clonotype assembly, diversity metrics, and integrated expression analysis.
09
Flexible Turnaround: Results delivered in 3–4 weeks, with expedited processing available.
This method is ideal for dissecting complex immune responses in oncology, infectious disease, vaccine development, and autoimmunity. Researchers use it to:
-
Oncology: Mapping T and B cell clonotypes and states in tumor microenvironments to identify therapy-responsive subsets.
-
Infectious Disease Research: Profiling pathogen-specific immune cells and their transcriptional responses.
-
Vaccine Development: Tracking clonal expansion and activation profiles to optimize vaccine formulations.
-
Autoimmune Disorders: Identifying autoreactive clones and revealing their gene expression signatures.
-
Translational Immunology: Connecting receptor specificity with cell function to guide therapeutic strategies.
-
Immune Cell Atlas Projects: Building comprehensive maps of immune diversity across tissues and conditions.
What is Single-Cell Immune Repertoire Sequencing Used For?
Single-Cell Immune Repertoire Sequencing with AUGenomics
Sample Submission
-
Accepted sample types: Fresh or cryopreserved single-cell suspensions from PBMCs, tumor, lymph node, or spleen
-
Input requirement: 10,000–50,000 viable cells recommended
-
Suggested sequencing: Full transcriptome + V(D)J receptor libraries using platforms like 10x Genomics
Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Standard turnaround is 3–4 weeks, depending on cell type and sequencing depth. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: Can I analyze TCR or BCR sequences together with gene expression?
A: Yes. This method captures both immune receptor sequences and transcriptomes from the same single cells, enabling rich co-analysis.
Q: What is the minimum number of cells required for meaningful results?
A: We recommend at least 10,000 high-viability cells to ensure robust data across immune subsets and clonal populations.
Q: Can this method detect rare antigen-specific clones?
A: Yes. Combining clonal tracking with cell surface markers and gene expression helps enrich for rare but relevant populations.
Q: Which sequencing platforms do you use?
A: We typically use Scale Biosciences, Parse Biosciences and CS Genetics.
Q: Do you support multi-omic integration?
A: Absolutely. We can combine receptor sequencing with surface protein or chromatin accessibility profiling for a multidimensional view.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
-
Single-cell RNA-seq: Sequencing of individual cells’ transcriptomes.
-
V(D)J sequencing: Capturing recombined TCR or BCR regions for repertoire profiling.
-
Transcriptomic profiling: Analyzing the full gene expression profile of each cell.
-
Clonal tracking: Monitoring the frequency and expansion of immune cell clones.
-
Immune heterogeneity: The variation in function, state, and type across immune cells.
