Dataset features

Specifications


Application: GRO-seq analysis
Number of samples: 2
Release date: Aug 15 2013
Last update date: Oct 18 2018
Access: Public
Diseases: Neoplasms, Prostatic Neoplasms
Chemicals: Androgens
Computational protocol: Bowtie2, BEDTools, edgeR
Dataset link LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [ChIRP-seq]

Experimental Protocol


Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq); ChIRP-seq data for a lincRNA (PCGEM1). LNCaP cells were grown to 30-50% confluence and siRNA/ASO transfections were carried out using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Control samples were transfected with scramble ASO and control siRNA, respectively. On the following day of transfection, the cells were cultured in UltraCULTURE (Phenol red free) + 5% Charcoal Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM for 1 hour we have sequenced the DNA sequences that are associated with the presence of a RNA molecule on a genome wide scale. PCGEM1 probe, -DHT PCGEM1 probe, +DHT

Repositories


GEO

GSE47804

ArrayExpress

E-GEOD-47804

ENA

SRP024668

BioProject

PRJNA207830

Download


Contact


MICHAEL ROSENFELD
MICHAEL G ROSENFELD

Dataset Statistics

info

Citations per year

Dataset publication