Single-cell RNA sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS). All single-cell mRNA sequencing data were acquired from a single patient (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). The PDX samples were mapped to the human and mouse genome, respectively. To remove the cells with low sequencing quality, we applied filtering criteria using nUMI, nGene, proportion of mitochondiral genes, and averaged expression of housekeeping genes. Additional filtering criteria was applied to the PDX samples to eliminate human-mouse mixed cells. Total 3,934 cells met the criteria. After identification of cell type, the strict criteria were applied to tumor cells using nGene and inferred copy number variations. Thereafter, we removed outliers in nGene to eliminate potential multiplets in nontumor cell population. The raw data at EGA archive due to patient privacy concerns [EGAD00001005978].