Dataset Information


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

ABSTRACT: 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 (to reduce the rRNA content) followed by library preparation using ScriptSeq. 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 (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) using the study ID EGAS00001001236 following request. An expression matrix of FPKM values are available without restriction at ArrayExpress.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens  

SUBMITTER: Jakob Hedegaard  

PROVIDER: E-MTAB-4321 | ArrayExpress | 2016-06-17



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Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma.

Hedegaard Jakob J   Lamy Philippe P   Nordentoft Iver I   Algaba Ferran F   Høyer Søren S   Ulhøi Benedicte Parm BP   Vang Søren S   Reinert Thomas T   Hermann Gregers G GG   Mogensen Karin K   Thomsen Mathilde Borg Houlberg MBH   Nielsen Morten Muhlig MM   Marquez Mirari M   Segersten Ulrika U   Aine Mattias M   Höglund Mattias M   Birkenkamp-Demtröder Karin K   Fristrup Niels N   Borre Michael M   Hartmann Arndt A   Stöhr Robert R   Wach Sven S   Keck Bastian B   Seitz Anna Katharina AK   Nawroth Roman R   Maurer Tobias T   Tulic Cane C   Simic Tatjana T   Junker Kerstin K   Horstmann Marcus M   Harving Niels N   Petersen Astrid Christine AC   Calle M Luz ML   Steyerberg Ewout W EW   Beukers Willemien W   van Kessel Kim E M KEM   Jensen Jørgen Bjerggaard JB   Pedersen Jakob Skou JS   Malmström Per-Uno PU   Malats Núria N   Real Francisco X FX   Zwarthoff Ellen C EC   Ørntoft Torben Falck TF   Dyrskjøt Lars L  

Cancer cell 20160616 1

Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease with widely different outcomes. We performed a comprehensive transcriptional analysis of 460 early-stage urothelial carcinomas and showed that NMIBC can be subgrouped into three major classes with basal- and luminal-like characteristics and different clinical outcomes. Large differences in biological processes such as the cell cycle, epithelial-mesenchymal transition, and differentiation were observed. Analysis of transcript v  ...[more]

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