Mouse peripheral blood mononuclear cells (PBMCs) pooled from C57BL/6 mice were obtained from C&M LabPro (part number 11121911). The cells were 84% viable (trypan blue stain).
Amplified cDNA were used to generate 5’ gene expression, TCR enriched, and Ig enriched libraries, following the Chromium Single Cell V(D)J Reagent Kits User Guide with Feature Barcode technology for Cell Surface Protein (CG000186).
All libraries were sequenced on an Illumina NovaSeq 6000 (NovaSeq software v1.6).
5’ Gene Expression Libraries
- Sequencing Depth: 5’ Gene Expression Library - 74,933 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 - 8,874
- UMI counts - 4,990
- Median genes per cell - 1,663
V(D)J Enriched Libraries
TCR Libraries
- Sequencing Depth: TCR Library - 50,571 read pairs per cell
- Sequencing Coverage: Read 1 - 26 bp i7 Index - 8 bp i5 Index - 0 Read 2 - 91 bp
The key cell metrics were:
- Cells detected - 849
- Reads mapped to any V(D)J gene - 53.2%
- Cells with productive V-J spanning pair - 59.2%
Ig Libraries
- Sequencing Depth: Ig Library - 19,337
- 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 - 4,405
- Reads mapped to any V(D)J gene - 88.4%
- Cells with productive V-J spanning pair - 82.2 %