Peripheral blood mononuclear cells (PBMCs) from a CMV seropositive donor, were obtained through a collaboration. Cells were stained with a panel of 12 dCODE™ Dextramer® reagents (Immudex) and 17 TotalSeq™-C antibodies (BioLegend). See details in the Application Note “Redefining Cellular Phenotyping: Comprehensive Characterization and Resolution of the Antigen-Specific T Cell Response”.
Cells were 81% viable by Trypan blue stain.
The PBMCs were sorted for CD4-/CD8+/dextramer+ T cells.
The same cDNA was used to generate gene expression and cell surface protein (vdj_v1_hs_sorted_cmvpos_5gex_protein) libraries.
Libraries were prepared following the Single Cell V(D)J Reagent Kits User Guide (CG000186 RevA).
- All cells collected from the sort were loaded, due to the expected low cell number an accurate count of loaded cells could not be performed
- 1,797 T cells expected based on CD3D/CD3E expressing fraction in 5’GEX data
- 1,783 T cells expected based on CD3+ fraction in antibody data (estimated by counting cells above a cut off at 50% of the log2 UMI counts)
- 1,475 cells detected with either single TRA or TRB or both
- 72.5% cells with productive V-J spanning (TRA,TRB) pair
- Sequenced on an Illumina HiSeq4000 with ~12,000 read pairs per cell
- 150bp read1 (including 16bp Chromium barcode, 10bp UMI, 13bp switch oligo and transcript), 150bp read2 (transcript), and 8bp I7 sample barcode read configuration