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Comprehensive Transcriptional Analysis of Early Stage Urothelial Carcinoma using whole transcriptome sequencing

The expression profile and sequence variants of 476 early stage urothelial carcinoma were studied using whole transcriptome sequencing. RNA-Seq libraries were prepared by Ribo-Zero treatment of total-RNA followed by library preparation using ScriptSeq (both Epicentre/Illumina). RNA-Seq libraries were paired-end sequenced (2x 101 bp) on Illumina HiSeq 2000 and the resulting fastq files were processed using tools from the Genome Analysis Toolkit (GATK and from the Tuxedo suite. Access to the sequence data (mapped and un-mapped bam and vcf files), containing person identifying information, needs signature on a controlled access form, and can be accessed at The European Genome-phenome Archive (EGA) following request. An expression matrice of FPKM values are available without restriction at ArrayExpress (E-MTAB-4321).

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001001939 Illumina HiSeq 2000 476
EGAD00001001940 Illumina HiSeq 2000 476
EGAD00001001941 476
Publications Citations
Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma.
Cancer Cell 30: 2016 27-42
Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer.
NPJ Genom Med 2: 2017 36
Sexual Dimorphism in Outcomes of Non-muscle-invasive Bladder Cancer: A Role of CD163+ Macrophages, B cells, and PD-L1 Immune Checkpoint.
Eur Urol Open Sci 29: 2021 50-58
A Multi-Gene Signature of Non-Muscle-Invasive Bladder Cancer Identifies Patients Who Respond to Immunotherapies Including Bacillus Calmette-Guérin and Immune Checkpoint Inhibitors.
Int J Mol Sci 25: 2024 3800