Human dissociated lymph node tumor cells of a 19-year-old male Hodgkin’s Lymphoma patient were obtained by 10x Genomics from Discovery Life Sciences. Whole transcriptome libraries were generated with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000315) and sequenced on an Illumina NovaSeq 6000.
The targeted libraries were generated using the Targeted Gene Expression Reagent Kits User Guide (CG000293) and Human Pan-Cancer Panel reagent (PN-1000247) 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 Pan-Cancer 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: 11,332 (targeted); 78,313 (WTA)
- Median Targeted Genes per Cell: 168 (targeted); 150 (WTA)
- Median Targeted UMIs per Cell: 559 (targeted); 522 (WTA)
- Mean UMI recovery ratio (targeted vs. parent): 1.128
- Pearson correlation of log10 UMI counts per gene: 0.995