10k Human A1101 PBMCs with EBV Spike In (BEAM-T)

Expanded HLA-A*11:01-restricted anti-EBV T cells with specificity for AVFDRKSDAK were generated in house from peripheral blood mononuclear cells (PBMCs), seropositive for EBV, sourced from Discovery Life Sciences. They were then labeled with a panel of two peptides (plus an HLA-A*11:01 control peptide) and sorted for CD8+/PE+ T cells as described in the Sample Prep User Guide for Reagent Assembly, Sample Labeling & Flow Sorting for Barcode Enabled Antigen Mapping (CG000595, Rev A).

These sorted cells were then combined with PBMCs from an HLA-A*11:01-restricted EBV seropositive donor (Discovery Life Sciences, ~10% anti-EBV T cells, ~90% EBV seropositive PBMCs).

Peptides:

• EBV: AVFDRKSDAK (BEAM Conjugate 3)
• CMV: NLVPMVATV (BEAM Conjugate 4)
• HLA-A*11:01 negative control peptide (BEAM Conjugate 5)

Gene Expression, Antigen Capture (BEAM-T), and VDJ-T amplified libraries were generated from the sorted cells as described in the Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide (CG000591, Rev A) and sequenced on an Illumina NovaSeq 6000.

Paired-end, dual indexing libraries were sequenced to the following depths:

• GEX: 66,571 mean reads per cell
• Antigen Capture (BEAM-T): 10,996 mean reads per cell
• VDJ-T: 31,391 mean reads per cell

Sequencing read configuration:

• Read 1: 26 cycles (16 bp barcode, 10 bp UMI)
• i5 index: 10 cycles (sample index)
• i7 index: 10 cycles (sample index)
• Read 2: 90 cycles (transcript)

Sequencing data were processed using Cell Ranger v7.1, with web summary and output files available below.

• Cells detected: 9,798
• Median genes per cell: 2,136
• Median UMIs per cell: 6,296

Low Antigen Capture (BEAM-T) median UMIs are expected when a low percentage of pure CD8+/PE+ T cells is present in a background of PE- cells.

This dataset is licensed under the Creative Commons Attribution license.