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TranscriptomicsTranscriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)
Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancerM-bM-^@M-^Sassociated ncRNA transcripts (PCATs) by ab initio assembly...
ORGANISM(S): Homo sapiens 
2011-08-02 | E-GEOD-25183 | biostudies-arrayexpress
TranscriptomicsChimeraScan: A tool for identifying chimeric transcription in sequencing data
Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts. Thre...
ORGANISM(S): Homo sapiens 
2011-09-01 | E-GEOD-29098 | biostudies-arrayexpress
UnknownPrevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer.
Not available
S-EPMC3753703 | biostudies-literature
GenomicsDNA Methylation Analysis of Prostate Cancer Cell Lines and Tissues Using Next Generation Sequencing

Aberrant DNA methylation changes are known to occur during prostate cancer progression beginning with precursor lesions. Utilizing fifty nanograms of genomic DNA in Methylplex-Next Generation Sequencing (M-NGS) we mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=...

phs000597.v1.p1 | EGA
TranscriptomicsSChLAP-1, a long non-coding RNA, antagonizes the SWI/SNF complex and coordinates aggressive prostate cancer.
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Homo sapiens 
2013-07-20 | E-GEOD-40386 | biostudies-arrayexpress
TranscriptomicssiRNA Knockdown of SWI/SNF complex proteins in prostate cancer cell lines
Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus siRNAs targeting SWI/SNF complex proteins (SMARCA2, SMARCA4, and SMARCB1). Goal was to determine the effect of SWI/SNF knockdown on gene expression in prostate...
ORGANISM(S): Homo sapiens 
2013-07-20 | E-GEOD-40384 | biostudies-arrayexpress
TranscriptomicsProstate cancer cell lines: non-targeting siRNA versus SChLAP1-siRNA treated
SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus SChLAP1-siRNA treatment. Goal was to determine the effect of SChLAP1 knockdown on gene exp...
ORGANISM(S): Homo sapiens 
2013-07-20 | E-GEOD-40383 | biostudies-arrayexpress
TranscriptomicsOverexpression of SChLAP1 versus LACZ in RWPE cells
SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the benign immortalized prostate cell line RWPE overexpressing two isoforms of the SChLAP-1 lncRNA compared with RWPE overexpressing LACZ. Our goal was to determine the effect of SChLA...
ORGANISM(S): Homo sapiens 
2013-07-20 | E-GEOD-40385 | biostudies-arrayexpress
GenomicsTargeting the MLL complex in castration-resistant prostate cancer [ChIP-seq]
Men who develop metastatic castration-resistant prostate cancer (CRPC) invariably succumb to the disease. The development and progression to CRPC following androgen ablation therapy is predominantly driven by unregulated androgen receptor (AR) signaling. Despite the success of recently approved ther...
ORGANISM(S): Homo sapiens 
2015-03-02 | E-GEOD-60841 | biostudies-arrayexpress
TranscriptomicsRNA-seq of hepatic biopsies taken from patients with chronic liver disease presenting with different aetiologies (HCV, FLD) and fibrosis stages.
To determine gene signatures associated with advanced liver fibrosis, we undertook RNA-sequencing of liver biopsies from patients presenting with different aetiologies (HCV or FLD) and fibrosis stages (n=69 patients). This dataset is part of the TransQST collection.
ORGANISM(S): Homo sapiens 
2018-07-28 | E-MTAB-6863 | biostudies-arrayexpress
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