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.
3 ways of initiating a project
- 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). This validation carries a one-time $500 fee.
- 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.
- 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.
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 ~$50 per well.
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.