Services | Single cell V(D)J analysis

Delivering immune insights at single cell resolution

High-resolution immune repertoire insights at the single cell level

Our iPair and iPair+ single cell immune sequencing technologies provide critical data on the physical cognate pairing of TCR or BCR chains within a single cell.

Step 1
Cell plating

Cells can be sorted into 96 well plates at our site or yours.

  1. At iRep: Send us your sorted cells in an Eppendorf tube, and we will single cell plate using a Sony SH800 flow cytometer. *2 hour minimum is required.
  2. In your lab: Sort cells in house with the iPair plating kit. One kit comes with two specialty treated iCapture plates and one hard-shell adaptor for single cell capture at your site. Additional plates can be added to your order.
Step 2
Step 3
Step 4
Data analysis


Our core single cell immune sequencing service

While bulk amplification coupled with NGS provides detailed, sequence-level insight into the immune system, information related to the cognate pairing of TCR and BCR chains is lost once RNA extraction is performed.

iPair is the first commercialized method for maintaining associated pairing of human or mouse TCR-alpha and TCR-beta chains, as well as human TCR-gamma and TCR-delta and BCR-IgH and BCR-K/L chain pairings from a single cell in the same reaction well. This sensitive method enables amplification of immune receptor heterodimers from a single cell using arm-PCR. Basic sequencing data analysis is performed using our iPair analyzer for comprehensive insights into genomic diversity cell by cell.

iPair Plating Kits are provided for single cell sorting at your site. Our iCapture Plates are specially treated for dry capture and are compatible with single cell plating methods such as FACs with low carry volume. One kit includes two iCapture plates, a plate adaptor, and sealing foils. Additional plates can be purchased at any time.


Our enhanced single cell immune phenotyping service

Our iPair+ option allows for enhanced phenotypic analysis of human or mouse single immune cells alongside TCR-alpha/beta VDJ pairing.

Human iPair+ can be initiated either by a Gene-Specific Panel or an Oligo DT panel. Mouse iPair+ is available through an Oligo DT panel only.

Arm-PCR technology is the foundation of iPair

Amplicon rescue multiplex PCR (Arm-PCR) uses hundreds of VDJ-specific primers in one reaction, semi-quantitatively and inclusively amplifying all of the expressed V(D)Js in B and T cells from a single sample for cost-efficient insights into the expressed immune repertoire.

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