UROSCANSEQ - Bladder Cancer RNA-sequencing data - Cohort 1 (n=662)

Stage-independent real-time subtype classification and comprehensive biopsy profiling of urothelial carcinomas by the Lund Taxonomy system Modern Pathology (10.1016/j.modpat.2026.100997) RNA sequencing and clinicopathological metadata from Cohort 1 (n=662) of the UROSCANSEQ prospective translational study (ISRCTN15459149), investigating RNA-seq-based molecular diagnostics for urothelial carcinoma in a Swedish patient population. Deposited files UROSCANSEQ_Cohort_1_Metadata.xlsx — Cohort metadata including clinicopathological variables. RNA-sequencing data (.RData) — Gene expression summarized to the protein-coding gene level using high-confidence transcripts. Filtered TPM format, annotated with either Ensembl IDs (n=17,857) or HGNC gene symbols (n=17,835), covering all 662 sequenced urothelial carcinoma biopsies. Batch-corrected geTMM format, available for 533 high-quality samples, annotated with either Ensembl IDs (n=17,687) or HGNC gene symbols (n=17,665). Unfiltered gene-level expression (.tsv) — TPM values, raw counts, and gene lengths derived from the nf-core/rnaseq STAR/Salmon pipeline (v3.14). All single-sample classifications and variable scores were calculated from the filtered TPM/Ensembl ID dataset. Important notes The raw and TPM data contain a pronounced batch effect between the two sequencing facilities (CMD and CTG, as denoted in the metadata), which should be accounted for in downstream analyses. Sample quality is indicated by the UC_index_Low_Quality / UC_index_High_Quality labels, derived from a combined assessment of QC variables. Contact Pontus Eriksson ([e-mail]), Fredrik Liedberg ([e-mail])This work was supported by the Swedish Cancer Society (CAN 2023/2807), Swedish Cancer Society (project number 22 1973 Pj 01 H), Swedish Research Council (2021-00859), Lund Medical Faculty (ALF), the Mrs. Bertha Kamprad Cancer Foundation (FBKS-2023-3-504, FBKS-2019-35, FBKS-2021-22), Skåne University Hospital Research Funds, Maud and Birger Gustavsson Foundation, Hjelm Foundation, The Cancer Research Fund at Malmö General Hospital, Skåne County Council’s Research and Development Foundation (REGSKANE-622351), Gösta Jönsson Research Foundation, the Foundation of Urological Research (Ove and Carin Carlsson bladder cancer donation), Sjöberg Foundation, Anna-Lisa and Sven-Eric Lundgren Research Fund, and Hillevi Fries Research Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847583. The funding sources had no role in the study design, data analyses, interpretation of the results, or writing of the manuscript. The authors would like to acknowledge Center for Molecular Diagnostics, Clinical Genomics Lund, SciLifeLab and Center for Translational Genomics, Lund University, for providing expertise and service with sequencing and analysis.