A Whole-Genome Atlas of 605 Urothelial Carcinomas

Dataset description This dataset comprises whole-genome sequencing (WGS), whole-exome sequencing (WES), bulk RNA sequencing (RNA-seq), and single-cell RNA sequencing (scRNA-seq) data generated from the Chinese Urothelial carcinoma Genomic Atlas (CUGA) project. Cohort overview The dataset includes 669 tumor samples from 497 patients with urothelial carcinoma. 1. Whole-genome sequencing (WGS) somatic mutations Somatic mutation data derived from WGS are provided for all tumor samples. Variants were identified using standardized pipelines and are provided in a compressed tabular format. File:CUGA_WGS_somatic_mutations_669samples_497patients.tsv.gz Content:Somatic mutation calls across 669 tumor samples (497 patients) 2. Copy number alteration (CNA) data Copy number profiles were inferred from WGS data using multiple algorithms. Files: CUGA_WGS_CNVkit_copy_number_segments_669samples.seg CUGA_WGS_FACETS_copy_number_segments_669samples.tsv Content:Segment-level copy number alterations across all tumor samples generated by CNVkit and FACETS, respectively. 3. Structural variation (SV) calls Structural variants were detected using multiple algorithms to ensure robustness, including Delly, Lumpy, Manta, and Svaba. Files: CUGA_SV_Delly_calls.zip CUGA_SV_Lumpy_calls.zip CUGA_SV_Manta_calls.zip CUGA_SV_Svaba_indel.zip CUGA_SV_Svaba_vcf_calls.zip Content:Structural variant calls generated by the corresponding tools. 4. Whole-exome sequencing (WES) somatic mutations Somatic mutations derived from WES data are provided for a subset of patients. File:CUGA_WES_somatic_mutations_MAF_226patients.txt.zip Content:Mutation Annotation Format (MAF) file containing somatic mutations for 226 patients. 5. Bulk RNA-seq expression data Gene expression levels were quantified from RNA-seq data and normalized as TPM. File:CUGA_RNAseq_expression_matrix_TPM.tsv Content:Gene-level expression matrix (TPM-normalized) 6. Single-cell RNA-seq data Single-cell transcriptomic data are provided as a Seurat object for downstream analysis. File:UC_scRNA_seurat_object.rds Content:Processed single-cell RNA-seq data, including expression matrices, cell annotations, and metadata Notes All data have been de-identified prior to release. Detailed methods, including sequencing platforms, alignment, variant calling, and filtering strategies, are described in the associated manuscript. Reference genome builds and software versions are provided in the manuscript. Contact For data access inquiries or additional information, please contact:Wei Lv ([e-mail])