Peripheral blood mononuclear cells (PBMCs) of a healthy donor, purchased from AllCells (Catalog #: PB001), 87% viable by Trypan blue stain. PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell).
The same cDNA was used to generate gene expression and cell surface protein (vdj_v1_hs_pbmc2_5gex_protein) and B cell Ig (vdj_v1_hs_pbmc2_b) specific libraries.
Libraries were prepared following the Single Cell V(D)J Reagent Kits User Guide (CG000186 RevA).
- ~17,000 total cells loaded
- 3,719 T cells expected based on CD3D/CD3E expressing fraction in 5’GEX data
- 3,847 T cells expected based on CD3+ fraction in antibody data (CD3+ antibody cells identified by gating on UMI counts relative to IgG1 isotype control)
- 3,308 cells detected with either single TRA or TRB or both
- 75% cells with productive V-J spanning (TRA,TRB) pair
- Sequenced on an Illumina HiSeq4000 with ~10,000 read pairs per cell
- 150bp read1 (including 16bp Chromium barcode, 10bp UMI, 13bp switch oligo and transcript), 150bp read2 (transcript), and 8bp I7 sample barcode read configuration