Long-read spatial transcriptomics of patient-derived clear cell renal cell carcinoma organoids identifies heterogeneity and transcriptional remodelling following NUC-7738 treatment (code)

Nanopore libraries were basecalled using dorado SUP model (v0.7.0) and processed through epi2me-labs/wf-single-cell (v2.2.0) to generate gene and transcript count matrices. Spatial barcode positions were obtained by converting tagged BAM files to FASTQ format (bam2fastq.sh) and running Space Ranger to extract tissue_positions.csv. Expression matrices were analyzed in Giotto Suite with QC filtering, Leiden clustering, and scran-based differential expression.