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TranscriptomicsIntegrative epigenomic analysis of differential DNA methylation in bladder cancer
Background Urothelial carcinoma of the bladder (UC) is a common malignancy. Although extensive transcriptome analysis has provided insights into the gene expression patterns of this tumor type, the mechanistic underpinnings of differential methylation remain poorly understood. Multi-level genomic da...
ORGANISM(S): Homo sapiens 
2015-05-28 | E-GEOD-58256 | biostudies-arrayexpress
TranscriptomicsDetailed analysis of 6p and 1q amplifications in urothelial carcinoma reveals SOX4 as an auxiliary target on 6p, and BCL9, CHDL1, MCL1, SETDB1, and HIF1B as putative targets on 1q.
Background: Previous array CGH analyses have revealed several recurring genomic alterations in urothelial carcinoma. The most common genomic amplifications occur at 6p22 and 1q21-24. The main target gene at 6p22 is believed to be E2F3. This gene is frequently co-amplified with CDKAL1 and SOX4 and th...
ORGANISM(S): Homo sapiens 
2013-08-30 | E-GEOD-40938 | biostudies-arrayexpress
TranscriptomicsDNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status
We assessed DNA methylation and copy number status of 27,000 CpGs in 149 urothelial carcinomas and integrated the findings with gene expression and mutation data. Methylation was associated with gene expression for 1,332 CpGs, of which 26% showed positive correlation with expression, i.e., high meth...
ORGANISM(S): Homo sapiens 
2012-08-31 | E-GEOD-33510 | biostudies-arrayexpress
TranscriptomicsIntegrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression)
Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma 131 primary bladder cancer tumor samples were analyzed on Illumina gene expression Bead Arrays.
ORGANISM(S): Homo sapiens 
2012-06-17 | E-GEOD-32548 | biostudies-arrayexpress
TranscriptomicsIntegrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)
Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma 146 primary bladder cancer tumor samples were analyzed on BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University ...
ORGANISM(S): Homo sapiens 
2012-06-17 | E-GEOD-32535 | biostudies-arrayexpress
TranscriptomicsProcessed RNA-seq of 95 lung adenocarcinoma samples
The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions. Libraries were prepared using the Illumina TruSeq stranded mRNA protocol and sequenced on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden. Demulti...
ORGANISM(S): Homo sapiens 
2026-02-08 | E-MTAB-16082 | biostudies-arrayexpress
TranscriptomicsA Molecular Taxonomy of Urothelial Carcinoma
Even though urothelial cancer (UC) is the fourth common tumor type among males, progress in treatment development has been deficient. Pathological assessment provides the urologists with only a broad classification, complicated by frequent disagreement among pathologist and the co-existence of diffe...
ORGANISM(S): Homo sapiens 
2012-05-23 | E-GEOD-32894 | biostudies-arrayexpress
GenomicsUromol_RNA_Dataset_map - samples
Mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
EGAD00001001939 | EGA
GenomicsUromol_RNA_Dataset_unmap - samples
Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
EGAD00001001940 | EGA
GenomicsUromol_RNA_Dataset_vcf - samples
Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
EGAD00001001941 | EGA
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