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])数据集说明 本数据集包含来自中国尿路上皮癌基因组图谱（Chinese Urothelial carcinoma Genomic Atlas, CUGA）项目产生的全基因组测序（WGS）、全外显子组测序（WES）、批量RNA测序（RNA-seq）以及单细胞RNA测序（scRNA-seq）数据。 队列概况 本数据集包含497名尿路上皮癌患者的669份肿瘤样本。 1. 全基因组测序（WGS）体细胞突变 为所有肿瘤样本提供了基于WGS得到的体细胞突变数据。变异通过标准化流程鉴定，并以压缩表格格式提供。 文件：CUGA_WGS_somatic_mutations_669samples_497patients.tsv.gz 内容：涵盖669份肿瘤样本（497名患者）的体细胞突变调用结果。 2. 拷贝数变异（CNA）数据 通过多种算法从WGS数据中推断得到拷贝数谱。 文件： CUGA_WGS_CNVkit_copy_number_segments_669samples.seg CUGA_WGS_FACETS_copy_number_segments_669samples.tsv 内容：分别由CNVkit和FACETS生成的所有肿瘤样本的片段级拷贝数变异数据。 3. 结构变异（SV）调用结果 为保证结果稳健性，使用包括Delly、Lumpy、Manta及Svaba在内的多种算法检测结构变异。 文件： 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 内容：对应工具生成的结构变异调用结果。 4. 全外显子组测序（WES）体细胞突变 为部分患者提供了基于WES数据得到的体细胞突变数据。 文件：CUGA_WES_somatic_mutations_MAF_226patients.txt.zip 内容：包含226名患者体细胞突变的突变注释格式（MAF）文件。 5. 批量RNA-seq表达数据 从RNA-seq数据中定量得到基因表达水平，并以TPM（每百万转录本数）进行标准化。 文件：CUGA_RNAseq_expression_matrix_TPM.tsv 内容：基因水平的TPM标准化表达矩阵。 6. 单细胞RNA-seq数据 提供了可用于下游分析的Seurat对象格式的单细胞转录组数据。 文件：UC_scRNA_seurat_object.rds 内容：经过处理的单细胞RNA-seq数据，包含表达矩阵、细胞注释及元数据。 注 所有数据在发布前均已完成去标识化处理。详细的实验方法，包括测序平台、序列比对、变异调用及过滤策略，详见相关论文。参考基因组版本及软件版本信息已在论文中给出。 联系方式 若需数据获取咨询或其他相关信息，请联系：吕伟（[e-mail]）