Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Contribution of WDR77 and p53 to androgen response in prostate cancer cells

ABSTRACT: To decipher the contribution of WDR77 and p53 to androgen-responsive gene expression, effect of siRNA-mediated silencing of WDR77 and p53 on expression of androgen-dependent genes was studied. Human LNCaP prostate cancer cells were transfected with individual siRNA SmartPools targeting WDR77 or p53 or a non-targeting siRNA SmartPool. Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (5nM) or vehicle. Three biological replicates were generated per treatment group. Forty-eight hours later, total RNA was isolated and processed for Illumina oligoarray analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Qiang Hu

PROVIDER: E-GEOD-66977 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of an SRF- and androgen-dependent gene signature in prostate cancer

Project description:The androgen receptor (AR) is the principal target for treatment of non-organ confined prostate cancer (PCa). Systems and bioinformatics approaches suggest that considerable variation exists in the mechanisms by which AR regulates expression of effector genes and point towards a role for secondary transcription factors (TFs) therein. We identified a novel indirect mechanism of androgen action in which effects of androgens on PCa cells are mediated by Serum Response Factor (SRF). To identify and characterize genes and cellular processes that are androgen-regulated in an SRF-dependent manner in PCa, Affymetrix HG-U133 Plus 2.0 GeneChip Array analysis was performed starting from RNA obtained from LNCaP cells in which androgen stimulation was combined with siRNA-mediated SRF silencing. To this end, LNCaP cells were seeded in 60 mm dishes at a density of 550,000 cells per dish in antibiotic-free medium. The next day, cells were transfected with siGenome SmartPool siRNA targeting SRF (Dharmacon, Lafayette, CO) or a custom-made control SmartPool targeting luciferase (LUC condition) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Forty-two hours after transfection, cells were treated with 5nM R1881 or ethanol vehicle. 3 biological triplicates were included per treatment group. Forty-eight hours later, cells were harvested in Trizol reagent (Invitrogen). RNA was isolated, purified on RNeasy columns (Qiagen, Germantown, MD) and checked for integrity by Agilent testing (Affymetrix, Santa Clara, CA). cDNA was generated and hybridized to Human Genome U133 Plus 2.0 arrays (Affymetrix) according to the manufacturer’s instructions at the Mayo Clinic Advanced Genomics Technology Microarray Shared Resource core facility.

2011-02-28 | GSE22606 | GEO

Identification of an SRF- and androgen-dependent gene signature in prostate cancer

2011-02-28 | E-GEOD-22606 | biostudies-arrayexpress

TALEN-Engineered AR Gene Rearrangements Reveal Endocrine Uncoupling of Androgen Receptor in Prostate Cancer

Project description:This experiment addressed the question of whether full length Androgen receptor and Androgen Receptor variant ARv567es have similar transciptional activities. The transcriptomes of R1-AD1, a AR full length expressing cell line, are compared in an AR on (1nM DHT) to an AR off (ethanol vehicle) state. R1-D567 was derived from R1-AD1 and modified with TALENs in such a way as to express only AR-V567es. The AR on and off states were induced with a control siRNA (AR on) or a siRNA targeting exon 1 (AR off). R-AD1 was cultured for 24 hours in either base RPMI media with 1nM DHT or ethanol vehichle and RNA extracted. R1-D567 cells were electroporated with control siRNA or siRNA targeting exon 1 of AR and allowed to recover 48 hours and then cultured in base media with 1nM DHT or ethanol for 24 hrs. Each conditon was done in triplicate.

2013-09-01 | E-GEOD-49196 | biostudies-arrayexpress

BRG1-dependent regulation of Wnt signaling pathway during skeletal muscle differentiation

Project description:RNA-seq analysis for C2C12 myoblasts knocked down for either only-BRG1 or only-BRM or both BRG1 and BRM. Cells were treated with an siRNA SMARTpools of four oligos each targeting either BRG1 (siGENOME mouse Smarca4 pool #M-041135-01-0020) or BRM (siGENOME mouse Smarca2 pool #M-056591-00-0020) or both. Control samples were treated with non-targeting scrambled oligos (siRNA SMARTpool ON-TARGETplus scrambled non-targeting pool # D-001810-10-20). siRNA pools were purchased from Dharmacon, Horizon Discovery Ltd., USA.

2023-06-24 | GSE196283 | GEO

FSTL1 promotes keratinocyte migration.

Project description:This study identifies FSTL1 as key component of intiating keratinocyte migration in skin Total RNA from N/TERT-1 keratinocytes transfected with a non-targeting siRNA or Smartpool siRNA against FSTL1 were subjected to microarray analysis

2013-03-02 | E-GEOD-41615 | biostudies-arrayexpress

Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines

Project description:The goal of this experiment was to compare the gene expression programs mediated by androgen/AR vs. constitutively active, truncated AR variants in castration-resistant CWR-R1 prostate cancer cells. Because constitutive activity of truncated AR variants can mask androgen/AR target genes, the androgen/AR transcriptional program was assessed by silencing the trucnated AR 1/2/3/CE3 variant with siRNA targeting AR exon CE3 and treating cells with vehicle (ethanol) or 1nM DHT. Similarly, because full-length AR activity can mask truncated AR variant target genes, the AR variant transcriptional program was assessed under castrate conditions by selectively silencing full-length AR with siRNA targeting AR exon 7, and comparing this profile with CWR-R1 cells transfected wtih siRNA targeting AR exon 1, which silences all AR expression (full-length and truncated AR variants). CWR-R1 cells were maintained under castrate conditions in long term culture in order to enrich for the population of cells harboring a 48kb intragenic deletion in AR intron 1. These late-passage CWR-R1 cells were electroporated with siRNAs targeting AR exon 1, AR exon 7, or AR exon CE3. Electroporated cells were seeded in RPMI 1640 medium containing antibiotics and 5% charcoal-stripped, steroid-depleted medium and allowed to recover for 48h. After this 48h recovery, electroporated cells were switched to serum-free RPMI 1640 with 1nM DHT or 0.1% ethanol (vehicle control) for an additional 24h prior to extraction of total RNA. Three independent biological replicates were performed.

2012-10-23 | E-GEOD-41784 | biostudies-arrayexpress

Contribution of WDR77 and p53 to androgen response in prostate cancer cells

Project description:To decipher the contribution of WDR77 and p53 to androgen-responsive gene expression, effect of siRNA-mediated silencing of WDR77 and p53 on expression of androgen-dependent genes was studied.

2016-03-01 | GSE66977 | GEO

U2OS LC MSMS upon siRNA-eIF4A3 or 5nM ActD treatment.

Project description:Proteome analysis in U2OS cells treated with siRNA against eIf4A3 or 5nM Actinomycin D.

2021-09-08 | PXD016005 | Pride

Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines

2012-10-23 | GSE41784 | GEO

VPRBP, a novel androgen receptor and OGT target is an essential mediator of cellular transformation in prostate cancer

Project description:Androgen receptor (AR) plays a central role in the development of prostate cancer. Increased expression of O-GlcNAc transferase (OGT) and O-GlcNAcylation are also implicated in metastatic prostate caner. We have identified VPRBP as a novel androgen-regulated gene and the stability of the encoded protein is regulated by OGT.VPRBP downregulation led to significant decrease in cell proliferation and p53 stabilization in LNCaPs. In this study, we employed chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) to identify changes in p53 binding to the genome in VPRBP knockdown LNCaPs compared to scrambled siRNA transfected control cells. Stabilization of p53 was associated increased p53 recruitment to the chromatin.

2022-09-22 | GSE169129 | 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