Human peripheral blood mononuclear cells (PBMCs) of a healthy donor were obtained from AllCells (part number: PB001). The cells were 87% viable (trypan blue stain). The cells were labeled with a panel of 14 TotalSeq™-C antibodies and 3 isotype controls (BioLegend).
Amplified cDNA from the labeled cells were used to generate 5' gene expression, cell surface protein, TCR enriched, and Ig enriched libraries, following the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 User Guide with Feature Barcode technology for Cell Surface Protein (CG000208).
The gene expression, cell surface protein, TCR, and Ig enriched libraries were sequenced on an Illumina NovaSeq 6000 (NovaSeq software v1.6).
5' Gene Expression + Cell Surface Protein Libraries
- Sequencing Depth: 5' Gene Expression Library - 49,285 read pairs per cell Cell Surface Protein Library - 11,697 read pairs per cell
- Sequencing Coverage: Read 1 - 28 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 91 bp
The key cell metrics were:
- Cells detected - 11,715
- UMI counts - 4,077
- Median genes per cell - 1,404
V(D)J Enriched Libraries
TCR Libraries
- Sequencing Depth: TCR Library -13,000 read pairs per cell
- Sequencing Coverage: Read 1 - 26 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 91 bp
The key cell metrics were:
- Cells detected - 6,648
- Reads mapped to any V(D)J gene - 78.5%
- Cells with productive V-J spanning pair - 84.5%
Ig Libraries
- Sequencing Depth: Ig Library - 11,925 read pairs per cell
- Sequencing Coverage: Read 1 - 26 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 91 bp
The key cell metrics were:
- Cells detected - 1,309
- Reads mapped to any V(D)J gene - 84.9%
- Cells with productive V-J spanning pair - 89.5%