Services  |  Single cell V(D)J Analysis


iPair+: Coupling single cell phenotypic data with repertoire analysis

iPair+ customizable human and mouse single cell immune sequencing panels include markers for
over 100 popular phenotypic genes

iPair+ helps you make connections between immune repertoire genotype and phenotypes.

With iPair+, you can choose from a large list of popular gene targets or customize your own. Our data analysis tools will help you interpret and present your phenotypic data through visualization tools such as T-SNE plots and heat plots.

Gene targets include markers for:

    • T cell related genes
    • Macrophage related genes
    • Dendritic cell related genes
    • Neutrophil related genes
    • Eosinophil related genes
    • Transcription factors
    • Surface markers
    • Cytokines
DNA samples are loaded to 96-well plate for PCR analysis

2 ways to use iPair+

  1. Coamplify using gene-specific primers in the same well as the VDJ receptor (human only)
  2. Amplify with oligo-dT primers followed by phenotypic sizing primers in a separate plate

Compare: Gene-specific Panel vs. Oligo DT panel

Gene-specific panel Oligo DT
Number of markers Up to 30 100+
Customization select any of the 30 available markers (validation required) additional markers can be added (validation required)*
Advantage Lower cost Control read depth
Data analysis T-SNE plots available T-SNE plots, frequency of RNA
UMI Not included Included

*Please request the target lists. There is one for gene-specific panel and one for oligo-dT.

The main advantage of using gene-specific primers is affordability. The oligo-dT approach requires the amplification process to be split into two plates: one for VDJ amplification, and one for phenotyping. While this does increase the price due to increased processing needs, it allows for more user control of the sequencing depth of the phenotypic targets. With the single plate, gene-specific approach, it is possible to lose VDJ pairing information, because the highly expressed phenotypic targets occupy too many sequencing reads. However, if you are going to include a relatively small number of phenotypic markers (<15), we would recommend the gene-specific approach.

A personalized phenotyping primer mix can also be made. Fee applies to every 20 plates or until the mix expires (whichever comes first). Oligo dT amplification fees apply. Additional sequencing recommended.

How to order

Please complete the form below and we'll get back to you shortly. Have specific questions? Please feel free to contact us.

iPair and iPair+ are registered trademarks of iRepertoire, Inc.