It is unclear how urothelial carcinoma of the urinary bladder change, genetically and phenotypically, as patients progress from recurrent non muscle-invasive (NMI) to muscle-invasive (MI) disease or disease that require radical cystectomy. This data set contains gene expression data from 200 samples in a longitudinal study of such patients. Overlap with previously GEO-published cohorts from our lab is described in the metadata. Overall design: Total RNA isolated from FFPE-blocks containing tissue from trans-urethral resection of the bladder extracted using the High Pure FFPET RNA isolation kit (Roche), assessed for quality using Nanodrop ND-1000, and labeled using SensationPlus FFPE Amplification and WT labeling kit. Labeled sample was hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix) at the SCIBLU genomics facility in Lund, Sweden. Several samples may be derived from different tumors from the same pateints, see publication and metadata. Tumor stage in this study was determined using available pre-operative information (pathological stage from radical cystectomy not considered). The full dataset of 200 CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.6.0). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol, log-transformed, and median centered for the final normalized data set. The patient-level and tumor-level overlap with previous GEO submissions and publications from our lab (GSE83586) is described in a dedicated column in the metadata.