Loupe cell browser

Single-cell RNA-seq data from both KP (n=2) and KPF₁F₂ (n=2) tumors were demultiplexed using the 10x cellranger mkfastq version 3.1.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI, and R2 sequence. Reads were aligned to the mouse genome (mm10 with custom CRE-ERT2 and FoxA1/2 individual exon references) and UMIs were generated using cellranger count 3.1.0 with expected-cells set to 8000 per library. For the KP sample without stromal depletion, expected-cells was set to 7500. QC reporting, clustering, and dimension reduction were performed for initial data evaluation in 10x Genomics’ Cell Loupe Browser (v5.0). For the KP sample without stromal depletion, we captured 5,963 cells total with 48,090 mean reads per cell and 1,488 median genes per cell. For the KP sample with stromal depletion, we captured 8,536 cells total with 25,593 mean reads per cell and 736 median genes per cell. For the KPF₁F₂ sample without stromal depletion, we captured 4,662 cells total with 55,589 mean reads per cell and 1,552 median genes per cell. For the KPF₁F₂ sample with stromal depletion, we captured 4,415 cells total with 60,226 mean reads per cell and 1,339 median genes per cell. Additional details of the primary Cell Ranger data processing can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview.