PBMCs from a Healthy Donor: Targeted-Compare, Immunology Panel
Single Cell Gene Expression dataset analyzed using Cell Ranger 4.0.0
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Human peripheral blood mononuclear cells (PBMCs) of a healthy female donor aged 25 were obtained by 10x Genomics from AllCells. 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 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 immunology 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: 13,211 (targeted); 69,859 (WTA)
- Median Targeted Genes per Cell: 177 (targeted); 170 (WTA)
- Median Targeted UMIs per Cell: 629 (targeted); 666 (WTA)
- Mean UMI recovery ratio (targeted vs. parent): 1.132
- Pearson correlation of log10 UMI counts per gene: 0.992
This dataset is licensed under the Creative Commons Attribution license.