Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative transcriptomic analysis of prostate cancer and matched normal tissue using RNA-seq

ABSTRACT: We used RNA-seq to interrogate prostate cancer specific gene fusions, alternative splicings, somatic mutations and novel transcripts.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22260 | GEO | 2011/05/02

SECONDARY ACCESSION(S): PRJNA128733

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparative transcriptomic analysis of prostate cancer and matched normal tissue using RNA-seq

Project description:We used RNA-seq to interrogate prostate cancer specific gene fusions, alternative splicings, somatic mutations and novel transcripts. We sequenced the transcriptome (polyA+) of 20 prostate cancer tumors and 10 matched normal tissues using Illumina GAII platform. Then we used bioinformatic approaches to identify prostate cancer specific aberrations which include gene fusion, alternative splicing, somatic mutation, etc.

2011-05-02 | E-GEOD-22260 | biostudies-arrayexpress

Complete transcriptomic landscape of prostate cancer in the Chinese population using RNA-seq

Project description:There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations. Three of the 14 tumors (21.4%) harbored a TMPRSS2-ERG fusion, and the low prevalence of this fusion in Chinese patients was further confirmed in an additional tumor set (10/54=18.5%). Notably, two novel gene fusions, CTAGE5-KHDRBS3 (20/54=37%) and USP9Y-TTTY15 (19/54=35.2%), occurred frequently in our patient cohort. Further systematic transcriptional profiling identified numerous long ncRNAs that were differentially expressed in the tumors. An analysis of the correlation between expression of long ncRNA and genes suggested that long ncRNAs may have functions beyond transcriptional regulation. This study yielded new insights into the pathogenesis of prostate cancer in the Chinese population.Cell Research advance online publication 21 February 2012; doi:10.1038/cr.2012.30.

2011-12-31 | E-MTAB-567 | biostudies-arrayexpress

Expression profile of localized primary prostate cancer samples and the matched normal tissues

Project description:To identify new oncogenic drivers in prostate cancer, we performed transcriptome analysis of localized primary prostate cancer samples and the matched normal tissues.

2021-05-01 | GSE114740 | GEO

Human prostate organoid generation and the identification of prostate development drivers using inductive rodent tissues

Project description:Mechanistic links between development and disease can be exploited to provide clues to the cellular signalling pathways that might become re-activated during adult pathogenesis such as those affecting the prostate. However, the mechanisms underpinning prostate development require further characterisation. Previously, our group developed novel methods to produce prostate organoids using induced pluripotent stem cells (iPSCs). Here, we show that the iPSCs can be fully differentiated into prostate organoids using neonatal rodent seminal vesicle mesenchyme (SVM) in vitro. Additionally, we elucidated molecular drivers of prostate induction through RNA-sequencing analyses of the rat urogenital sinus (the embryonic precursor of the prostate gland) as well as the neonatal seminal vesicles. We identified candidate drivers evident in the inductive mesenchyme and epithelium involved with prostate specification. Our top candidates included Spx, Trib3, Snai1, Snai2, Nrg2, and Lrp4. This work lays the foundations to further interrogate the reactivation of developmental genes in adulthood, leading to prostate disease.

2023-07-05 | GSE234252 | GEO

Transcriptome profiling of Normal and Cancerous Prostate Cells using Affymetrix Human Transcriptome Array 2.0

Project description:To identify aberrant expression of transcripts in prostate cancer, we performed global gene and transcript expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP using Affymetrix Human Transcriptome 2.0 expression arrays.

2018-09-01 | GSE62497 | GEO

Genes associated with prostate cancer are differentially expressed in African American and European American men (matched normal specimens)

Project description:A total of 1,507 probes measured the expression of 517 genes on the custom Illumina DASL assay testing if select genes showed cancer-specific differential expression according to race. Genes were chosen for inclusion in the assay based on existing evidence from the literature and our own data for their importance to prostate cancer, prostate cancer aggressiveness, or cancer in general

2013-01-31 | GSE41968 | GEO

Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples

Project description:Prostate adenocarcinoma and matched adjacent normal samples were profiled by deep transcriptional sequencing to analyze transcription-induced chimeras and gene fusions. Reference samples from the MAQC and brain and universal reference libraries were also sequenced. Two-condition experiment plus reference samples: Prostate adenocarcinoma versus matched normal from three separate patients, plus brain and universal reference samples from the MAQC project.

2010-09-23 | E-GEOD-24283 | biostudies-arrayexpress

Normal and Cancerous Prostate Cells

Project description:This SuperSeries is composed of the following subset Series: GSE38674: Genomic DNA in Normal and Cancerous Prostate Cells GSE38676: Expression Analysis of Normal and Cancerous Prostate Cells GSE38677: Mapping of Transcription Start Sites of Normal and Cancerous Prostate Cells GSE38682: H3K4me3 Marks in Normal and Cancerous Prostate Cells GSE38683: H3K27me3 Marks in Normal and Cancerous Prostate Cells GSE38684: Chromatin Looping of Normal and Cancerous Prostate Cells Refer to individual Series

2012-10-16 | E-GEOD-38685 | biostudies-arrayexpress

Haploinsufficiency of interstitial genes between TMPRSS2 and ERG contributes to prostate tumorigenesis

Project description:TMPRSS2-ERG gene fusions that are frequently identified in prostate cancer can be generated either through chromosomal translocation or via interstitial deletion. The latter mechanism deletes an interstitial region of ~3Mb and it remains largely unanswered whether genes deleted within this region contribute to prostate cancer. By characterizing two knockin mouse models recapitulating TMPRSS2-ERG fusions with or without the interstitial deletion, we found that only those with deletion developed poorly differentiated adenocarcinomas with epithelial-to-mesenchymal transition, when under a Pten-null background. We identified several interstitial genes, including ETS2 and BACE2, whose reduced expression correlates with worse disease-free survival and lethal disease. By using an Ets2 conditional knockout allele, we demonstrated that loss of one copy of Ets2 was sufficient for prostate cancer progression when under a Pten-null background. Collectively, our data suggest that ETS2 is a prostate tumor suppressor and haploinsufficiency of one or more interstitial genes contributes to prostate cancer progression.

2015-12-31 | GSE63070 | GEO

Normal vs. Tumor Prostate miRNA

Project description:Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies

2006-04-05 | GSE4574 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data