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Homo sapiens

ABSTRACT: RNA-seq analysis of SLIRP knockdown with 1nM DHT in LNCaP cells

PROVIDER: PRJNA311699 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3161980.fastq.gz	Fastqsanger.gz
	SRR3161981.fastq.gz	Fastqsanger.gz
	SRR3161982.fastq.gz	Fastqsanger.gz
	SRR3161983.fastq.gz	Fastqsanger.gz
	SRR3161974.fastq.gz	Fastqsanger.gz

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Project description:LNCaP cells in response to DHT stimulation and inhibition/knockdown of TOPO2B

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LNCaP cells in response to DHT stimulation and inhibition/knockdown of TOPO2B

Project description:Microarray experiments were carried out to ascertain whether TOP2Î² is required for DHT induced androgen receptor target gene expression. We investigated the effect of pharmacological inhibition or RNA interference-mediated depletion of TOP2Î² on gene expression in androgen-dependent LNCaP prostate cancer cells. Analysis of gene expression in LNCaP cells under various conditions including serum starvation, DHT treatment, and DHT treatment combined with TOPO2B pharmacological inhibitors (Merbarone and Etoposide) and TOPO2B-shRNA knockdown.

2010-07-29 | E-GEOD-19445 | biostudies-arrayexpress

RNA-seq analysis of SLIRP knockdown with 1nM DHT in LNCaP cells

Project description:The purpose of this study was to profile gene expression changes that could occur with the loss of co-repressor SLIRP. In addition, we wanted to investigate how DHT could further alter gene expression. Methods: LNCaP cells were transfected with custom nonsense control siRNA or a pool of SLIRP siRNA (HSS130109, HSS188666, HSS188667 Invitrogen, Carlsbad, CA) at 40nM for 24hrs. Cells were washed once with PBS and replaced with SFM containing EtOH or 1nM/ml DHT for another 24hrs. Two biological replicates were collected from 2 different experiemnts for total of 4 replicates. RNA collected was sequenced using Illumia HiSeq2000 single read 50 bp by the HTSF core at UNC and aligned and normalized by the Bioinformatics core at UNC. Results: We found a differential gene expression pattern between our control and SLIRP knockdown samples. We also identified a 176 AR gene signature with 3 subclasses and a large SLIRP gene signature (~1700).

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FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells (HTS)

Project description:We report the androgen receptor recruitment to the chromatin of androgen responsive prostate cancer cell lines, LNCaP-1F5 and VCaP in response to physiological androgen 5a-dihydrotestosterone (DHT) using ChIP-sequencing. We compare the AR recruitment by DHT to that by partial agonist/antagonist cyproterone acetate (CPA), mifepristone (RU486) and bicalutamide (Bica) in LNCaP-1F5 cells. We also report the role of glucocorticoid receptor recruitment in presence of dexamethasone (Dex) in androgen responsive prostate cancer cells. The AR and GR cistrome analysis is subsequently compared with gene expression data and RNA Pol II analysis. The ChIP-seq has been performed using AR, GR, RNA Pol II antibodies. Examination of AR and GR binding sites in LNCaP-1F5 and VCaP cells in presence of DHT and Dex respectively. Further analysis of AR binding sites in LNCaP-1F5 cells treated with partial agonist/antagonists, CPA, RU486 and Bica. Additionally RNA Pol II mapping is performed in cells treated with DHT and Dex.

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