A single chromosome 3p break initiates clear cell renal cell carcinoma evolution (processed data files)

Intermediate R data objects — single-cell CITE-seq analysis of chromosome 3p loss in RPTECs============================================================================================ These are the intermediate R objects needed to reproduce the single-cell analysisfigures without re-running the pipeline from raw FASTQ. They sit between theCell Ranger output (deposited at GEO) and the manuscript figures. Related resources------------------ Analysis code: https://github.com/S-Zhang-Lab/Chromothripsis_RD_PL- Raw FASTQ + Cell Ranger matrices: GEO accession GSEXXXXXX (replace with the assigned accession) Software--------R 4.3.2; Seurat v5; inferCNV; GSVA. Objects were written with saveRDS()/save.image().Load .rds with readRDS("<file>"); load .RData with load("<file>"). Files-----integrated_obj.rds Integrated Seurat object for all three lanes (L1+L2+L3), after HTO demultiplexing and integration. This is the entry point for the analysis. Produced by: Rscript/01_integration_lanes.R Post_inferCNV_obj.rds The integrated Seurat object with inferCNV copy-number results merged back into the metadata. Used to classify chromosome 3p-loss cells. Produced by: Rscript/02_InferCNV_integrated.R Backs Supplementary Figure 5A-C (inferCNV heatmap, % 3p-loss cells, Chr3 fold change). day5_cells_EA.rds / day10_cells_EA.rds Day-5 and Day-10 cell subsets used for differential expression and GSVA. Produced by: Rscript/04_DEG_loss_analysis.R (read by 04 and 05) Back the Chromosome 3p-loss DEG volcano plots, Supplementary Figure 5D (Day 5) and 5E (Day 10). Day5_gsvasc.rds / Day10_gsvasc.rds GSVA / ssGSEA score objects for Day 5 and Day 10. Produced by: Rscript/05_GSVA_loss_analysis.R 03_3p_loss.RData Full R session image from the karyoploteR / 3p-loss classification step, including the final chromosome 3p-loss cell assignments. Produced by: Rscript/03_karyoploteR.R (load with load("03_3p_loss.RData")) Notes------ Cell Ranger filtered matrices and raw FASTQ are NOT included here; they are at GEO.- inferCNV pipeline step files (01_incoming_data ... 15_tumor_subclusters .infercnv_obj) are regenerated automatically by inferCNV and are intentionally not archived.