Sorted PBMCs from a CMV seropositive donor - TCR enrichment from amplified cDNA

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

This dataset is licensed under the Creative Commons Attribution license.