Supplementary Tables 1-24 from Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment

Table_S1. Study cohort. Table_S2. The sample composition of each dataset. Table_S3. Patient information. Table_S4. Whole genome sequencing (WGS) datasets. 1,411 UC whole genomes. Table_S5. Whole exome sequencing (WES) datasets. Table_S6. RNA sequencing (RNA-seq) datasets. Table_S7. Circle-seq datasets. Table_S8. Single-cell RNA-seq (scRNA-seq) datasets. Table_S9. Amplicon classification. Table_S10. Amplicon similarity scores. Table_S11. ecDNA prevalence in human cancers. Table_S12. Genomic and sequence features of amplicons. Table_S13. Oncogene list. Table_S14. Genes encoded on all focal amplifications. Table_S15. ecDNA status and CNV ITH in tumor multi-region sampling cohort. Table_S16. Diver gene alterations in ecDNA- and ecDNA+ tumors. Table_S17. Summary of Single-cell RNA-seq (scRNA-seq) data. Table_S18. IHC evaluation of CD45 in 19 tumors with scRNA-seq data. Table_S19. Signature genes of 50 robust NMF programs. Table_S20. Pathway enriched in each NMF program. Table_S21. Top 30 signature genes of tumor meta-program. Table_S22. Differential pathways of malignant cells between ecDNA- and ecDNA+ tumors. Table_S23. Gene signature matrix for deconvolution analysis of bulk RNA-seq data. Table_S24. Software.