Single-Cell Immune Profiling

Explore the immune system at single-cell resolution

The immune system is a complex, vital network that includes various organs, cell types, and molecules. Two important components of this complex network are the T- and B-cells with their corresponding T-cell receptors (TCRs) and B-cell receptors (BCRs). BCRs recognize antigens leading to activation and subsequent antibody secretion of the cells. TCRs recognize antigens presented by other cells and, therefore, play a vital role in discriminating pathogenic antigens from host antigens. Due to the somatic rearrangement of the B- and T-cell receptor genes, which is also known as V/D/J recombination, a vast number of unique receptors for the detection of various antigens is build. This V/D/J recombination results in an individual’s TCR and BCR repertoire.

Investigating the diversity of immune cells with respect to the TCR and BCR repertoires provides insights into the functioning of our immune system and its response to different conditions. Thus, studies at single-cell resolution using RNA sequencing allow the identification of different clonotypes and clone-specific gene expression. Since a functioning immune system is essential for our health, insights are of high relevance and a better understanding of the immune system composition can help to better understand the complexity of diseases and to develop and test appropriate therapies or vaccines.

Application areas of single-cell immune profiling:

  • Response to different conditions and therapeutic interventions
  • Vaccination and therapy development
  • Target specificity of different clonotypes
  • Investigation of autoimmune diseases

We help you to explore your samples’ immune cell diversity by providing Single-Cell Immune Profiling (SIP).

CeGaT Is the Best Partner for Sequencing Your Project

High
Flexibility

Scalable for different sample types, quantities, and requirements

Accredited
Procedures

Processing according
to highest quality
standards

Outstanding
Customer Service

Constant scientific supervision of all
project steps

Quality
Made in Germany

In-house processing to maintain our reliable and trusted quality

Our Commitment to You

Fast Processing

Turnaround time
≤ 15 business days

High Quality

Highest accuracy for all processes

Secure Delivery

Secure provision of sequenced data via in-house servers

Safe Storage

 Safe storage of samples and data after project completion

Our Service

We provide a comprehensive and first-class project support from selecting the appropriate product to evaluating the data. Each project is supervised by a committed scientist. You will have a contact person throughout the whole project.

Our service includes

  • Detailed project consulting
  • Product selection tailored to your project
  • Detailed bioinformatic evaluation of your data
  • Detailed project report with information about sample quality, sequencing parameters, bioinformatic analysis, and results

Benefit from our dedicated support and accredited workflows.

Explore Our Product Portfolio for Single-Cell Immune Profiling

We offer Single-Cell Immune Profiling (SIP) using the 10x Genomics® Chromium™ system and the latest NGS technology. The immune-specific regions of the α- and β- chains (TCR) and Ig-chains (BCR) are provided as paired sequences. Would you like to have bioinformatic analyses performed on your data in addition to the included deliverables? Each of our products can be supplemented with further services. We are happy to advise you.

SIP B-Cell

Species
Human, mouse

Sample type
Frozen single cell suspensions

Sample requirements
1 million cells in 1 ml cryopreservation medium
> 90% cell viability
Other samples might be possible upon request

Target
Gene expression
+ BCRs

Platform
Chromium™ system (10x Genomics®)
Illumina

Output
Flexible

Included deliverables
Project report & FASTQ files

SIP T-Cell

Species
Human, mouse

Sample type
Frozen single cell suspensions

Sample requirements
1 million cells in 1 ml cryopreservation medium
> 90% cell viability
Other samples might be possible upon request

Target
Gene expression
+ TCRs

Platform
Chromium™ system (10x Genomics®)
Illumina

Output
Flexible

Included deliverables
Project report & FASTQ files

SIP Combined

Species
Human, mouse

Sample type
Frozen single cell suspensions

Sample requirements
1 million cells in 1 ml cryopreservation medium
> 90% cell viability
Other samples might be possible upon request

Target
Gene expression
+ BCRs
+ TCRs

Platform
Chromium™ system (10x Genomics®)
Illumina

Output
Flexible

Included deliverables
Project report & FASTQ files

If you are generally interested in single-cell sequencing, please check our Single-Cell RNA Sequencing portfolio.

Bioinformatics

Raw sequencing data are automatically processed. We offer different levels of bioinformatic analysis. The default level is Level 1. With increasing bioinformatic level, more data are delivered. All higher levels include the data from the lower levels. In addition to the data, and independent of the analysis level, a project report is generated.

We analyze your Single-Cell Immune Profiling data with the Cell Ranger software from 10x Genomics®. This workflow includes read alignment, filtering, gene expression analysis, and clonotype calling on the V/D/J libraries.

Level 1:

  • Demultiplexing of the sequencing data, including index reads (FASTQ format)

Level 2:

  • Mapping of the sequencing data
  • Gene expression analysis
  • V/D/J analysis

Level 3:

  • For more than one sequenced sample, your Single-Cell Immune Profiling data is combined into an experiment-wide matrix and reanalyzed after normalization.

Our Workflow

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Support & Offer

Support &
Offer

Icon process flow
Icon process flow

Sample Receipt & Quality Control

Icon process flow
Icon process flow

Library Preperation & Sequencing

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Bioinformatic Analysis & Data Delivery

Technical Information

We can process between 500 – 10,000 cells per sample, and up to 8 samples can be run in parallel on one Chromium Next GEM Chip. The immune-specific regions of the α- and β- chains (TCR) and Ig-chains (BCR) are preserved and provided as paired sequences. It is recommended to sequence at least 20,000 paired-end reads per cell for the gene expression. For the TCR and BCR libraries, at least 5,000 paired-end reads per cell are recommended. The required sequencing depth strongly depends on the sample type and on the experimental question.

At CeGaT, sequencing is performed using the Illumina sequencing platforms. If you require other sequencing parameters, please let us know! We can provide further solutions.

Further Information about Single-Cell Immune Profiling

Our immune system defends the body against many pathogens to protect us from diseases. These pathogens range from viruses to bacteria, parasites, fungi, toxins, and cancer cells. An extensive network of organs, cells, proteins, and chemicals work together to protect us from infections. Our human immune system consists of two parts: the innate and the adaptive immune system. The innate immune system’s response is a non-specific, immediate response that does not form an immunological memory. In contrast, the adaptive immune system responds specifically to antigens or pathogens. However, This specific response takes time, causing a lag phase between exposure and the adaptive immune response. The adaptive immune system forms an immunological memory, allowing faster and more potent immune responses against the memorized pathogen.

White blood cells play a fundamental role in the adaptive immune system as they circulate in the bloodstream or reside in tissue to attack and destroy pathogens. A subtype of white blood cells is the lymphocytes, namely the T- and B-cells with their respective receptors on the cell surface, the T-cell receptors (TCRs) and B-cell receptors (BCRs).

The TCR is a membrane-bound protein complex. It binds antigens presented by MHC molecules and activates the T cell. The TCR is comprised of an alpha and a beta peptide chain. A disulfide link connects these two chains. The subunits consist of variable (V) and constant (C) regions. The TCR is formed with the transmembrane protein CD3 and two zeta polypeptides. A minor fraction of T cells comprises gamma and delta chains instead of alpha and beta chains.

The variable regions of the alpha and beta chains each have three hypervariable or complementarity-determining regions (CDRs). The CDR3 is the central region to recognize processed antigens. To identify as many antigens as possible, the TCR repertoire is highly diverse. Its diversity originates from recombination, more precisely, the V(D)J recombination, where variable (V), joining (J), and diversity (D) gene segments are randomly rearranged. This V(D)J recombination allows the recognition of almost all pathogens.

However, V(D)J recombination is not only a pivotal part of the development of the TCR repertoire; it is also responsible for the highly diverse repertoire of antibodies. The antibody molecules, including the B-cell receptors, comprise a heavy and light chain. As for the TCRs, the subunits consist of variable (V) and constant (C) regions. Additionally, they contain joining (J) gene segments. The heavy chains also include diversity (D) gene segments. By this recombination, at least 1011 different antibody molecules are formed.

With single-cell immune profiling, the B-cell receptor and T-cell receptor sequences can be sequenced and analyzed at a single-cell resolution. Hundreds to tens of thousands of cells can be analyzed in a single run. In addition to the analysis of the complete immune repertoire, the gene expression of the T and B cells can be investigated, giving insights into the adaptive immune system at single cell level. Single-cell immune profiling helps you explore your samples’ immune cell diversity and increase the understanding of the adaptive immune system.

Downloads

Single-Cell Immune Profiling Flyer (EN)

Contact Us

Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.

Start Your Project with Us

We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.

When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.