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 was used to generate TCR 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).
The libraries were sequenced on an Illumina NovaSeq 6000 (NovaSeq software v1.6).
Note: The web summary will have a Warning alert for TCR library. This is due to the low fraction of T cells in mouse PBMC and the low expression levels of TCR-α and TCR-β genes in these cells.
V(D)J Enriched Libraries
TCR Libraries
- Sequencing Depth: TCR Library - 48,868 read pairs per cell
- Sequencing Coverage: Read 1 - 150 bp i7 Index - 8 bp i5 Index - 0 Read 2 - 150 bp
The key cell metrics were:
- Cells detected - 848
- Reads mapped to any V(D)J gene - 44.5%
- Cells with productive V-J spanning pair - 60.4%
Ig Libraries
- Sequencing Depth: Ig Library - 19,283
- Sequencing Coverage: Read 1 - 150 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 150 bp
The key cell metrics were:
- Cells detected - 4,395
- Reads mapped to any V(D)J gene - 85.5%
- Cells with productive V-J spanning pair - 82.3 %