Services  |  Single cell V(D)J Analysis


iPair: Our core single cell immune sequencing service

When RNA is extracted for bulk repertoire sequencing, information related to the cognate pairing of BCR and TCR chains is lost. Our single cell service, iPair, is the first consumer-based service specifically designed for capturing physically paired variable regions in T cells and B cells.

Bulk repertoire sequencing as compared to single sell sequencing. In bulk sequencing, V(D)J RNA is amplified and sequenced together from multiple B and T cells. Single cell sequencing preserves information about individual paired chains in each well during sequencing.

3 ways of initiating a project

  1. If you have access to FACS with single cell capability, you can single cell plate at your site using the iPair Plating Kit.
    Note: It is highly recommended to perform a compatibility check using a known cell type (we recommend Jurkat cells).Validation fees may apply.
  2. Alternatively, you can magnetically sort or use FACS to bulk sort into QIAgen’s RNAprotect Cell Reagent. Cells will be single cell plated at iRepertoire’s service laboratory. This option is ideal if you want bulk amplification alongside iPair services.
  3. If you lack sorting capability, or prefer this step to be handled by iRepertoire, a project consultation is required. Please see our Sample Processing page to see the extent of our cell handling services.
Automation in the laboratory. Pipetting robot pipettes into a 96-well plate

Other ways to use iPair

If you don’t need single cell resolution, but you have limited cell numbers, you can by-pass losses due to RNA extraction by plating more than 1 cell per well (up to 100 per well) and retrieve information for both loci from the same reaction. For instance, for 1,000 cells, you may decide to plate 10 cells per well.

Do you have cell lines that you would like to sequence? iPair is a great option.We can accept cell line RNA and use the iPair system to co-amplify the receptor pair for a competitive price.

Sample submission requirements

iPair Sample Submission Requirements | Single cell V(D)J analysis

Single Cell Plating at iRepertoire’s Site Staining, Single Cell Sorting and Plating (Includes Indexed Sorting)** Sorting At Your Site and Submitting Plates to iRepertoire
Submission cell type Sorted cells Bulk population (i.e., PBMC) Sorted and/or plated cells
Minimum cell amount 1000 cells* 1 x 106 cells ½ of 96-well iCapture plate
Minimum cell concentration 5 cells / uL 3 x 106 cells/mL N/A
Minimum Volume 200 uL ~300 uL N/A
Optimum Cell Amount 10,000 cells or more 5 x 106 cells/mL N/A
Optimum Cell Concentration 50 cells / uL 5 x 106 cells/mL N/A
Optimum Volume 200 uL 1 mL N/A
Required cell viability N/a if stored immediately post-sort in recommended storage buffer 75% or greater N/A
Shipping conditions 4°C or dry ice Dry ice Dry ice
Recommended Storage Buffer QIAgen RNAprotect Cell Reagent (Cat. No. 76526) CryoStor CS10 cryopreservation media or similar Requires the use of iPair Plating Kit

*Requires a control sample of similar cell type in requested storage buffer for FACS gating.
**Amount of cells reflected in able depends on cell subset(s) requested – more cells may be required. Project  specific amounts require consultation to determine project parameters.

How to order

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