All datasets

10k Human A0201 PBMCs with CMV, Flu, and SARS-Cov2 Spike In (BEAM-T)

Universal 5' Gene Expression dataset analyzed using Cell Ranger 7.1.0

Assess data quality
View summary metrics to assess data quality and more.
View summary
Visualize and explore data
Discover differentially expressed genes, visualize your favorite genes, and explore your data with our visualization software.

Learn about Chromium analysis

The following cells, at the specified percentages, were combined with peripheral blood mononuclear cells (PBMCs) from an HLA-A*02:01-restricted CMV seropositive donor (sourced from Cellero):

  • 40% expanded HLA-A*02:01-restricted anti-CMV T cells (generated from PBMCs sourced from Cellular Technologies Limited) with specificity for NLVPMVATV
  • 10% anti-Flu T cells (Charles River/Hemacare) with specificity for GILGFVFTL
  • 5% anti-SARS-CoV-2 T cells (Charles River/Hemacare) with specificity for KLPDDFTGCV

Cells were labeled with a panel of five peptides, plus an HLA-A*02:01 negative control peptide, and were then 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).

Peptides:

  • CMV: NLVPMVATV (BEAM Conjugate 10)
  • EBV-BRLF: YVLDHLIVV (BEAM Conjugate 11)
  • Flu: GILGFVFTL (BEAM Conjugate 12)
  • EBV-BMLF: GLCTLVAML (BEAM Conjugate 13)
  • SARS-CoV-2: KLPDDFTGCV (BEAM Conjugate 14)
  • HLA-A*02:01 negative control peptide (BEAM Conjugate 15)

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 User Guide (CG000591, Rev A) and sequenced on an Illumina NovaSeq 6000.

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

  • GEX: 25,730 mean reads per cell
  • Antigen Capture (BEAM-T): 2,972 mean reads per cell
  • VDJ-T: 10,957 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 in relevant tabs.

  • Cells detected: 9,573
  • Median genes per cell: 2,417
  • Median UMIs per cell: 5,988

This dataset is licensed under the Creative Commons Attribution license.