Study

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

Study ID Alternative Stable ID Type
EGAS00001001236 Other

Study Description

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).

Study Datasets 3 datasets.

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Dataset ID Description Technology Samples
EGAD00001001939
Mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
Illumina HiSeq 2000 476
EGAD00001001940
Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
Illumina HiSeq 2000 476
EGAD00001001941
Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
476

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