Human peripheral blood mononuclear cells (PBMCs) of a healthy female donor aged 29 were obtained by 10x Genomics from AllCells. The whole transcriptome (parent) library was prepared with Chromium Single Cell V(D)J Reagent Kits User Guide (v1 Chemistry) with Feature Barcoding technology for Cell Surface Protein Rev A (CG000186) and sequenced on an Illumina NovaSeq 6000. The targeted gene expression libraries were generated with Targeted Gene Expression Reagent Kits User Guide (CG000293) using the Human Immunology Panel (PN-1000246) and sequenced on an Illumina NovaSeq 6000.
The targeted-compare pipeline in Cell Ranger 4.0 was used to compare the parent whole transcriptome analysis (WTA) with the Human Immunology Panel targeted analysis. While it is not necessary to compare the WTA and targeted data when doing targeted gene expression, if both the targeted and parent samples have been sequenced, the targeted-compare pipeline may be used to compare the two samples.
Key metrics were:
- Mean sequencing reads per cell: 10,271 (targeted); 71,416 (WTA)
- Median Targeted Genes per Cell: 128 (targeted); 124 (WTA)
- Median Targeted UMIs per Cell: 364 (targeted); 379 (WTA)
- Mean UMI recovery ratio (targeted vs. parent): 1.104
- Pearson correlation of log10 UMI counts per gene: 0.998