Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Duke DNase-seq in LNCaP

ABSTRACT: We collected DNase-seq data in LNCaP cells (human prostate adenocarcinoma cell line) before and after 45 minutes and 4 hours of 1 nM R1881 treatment. We then used these DNase-seq data to predict the quantitative TF occupancy with our statistical method (TOP) and examine how their occupancy changes genome-wide across treatment conditions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE157473 | GEO | 2020/09/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide RNA-sequencing (RNA-seq) of benign and malignant prostate cell lines without and with androgen (R1881) stimulation.

Project description:RNA-seq data were obtained from hTERT immortalized human prostate transit amplifying EP156T cells (+/- 10 nM R1881 for 48 hrs), progeny tumorigenic EPT3-M1 cells recovered from mouse metastatic tumor (+/- 10 nM R1881 for 48 hrs) and the prostate cancer cell lines LNCaP (+/- 10 nM R1881 for 48 hrs), VCaP (+/- 1 nM R1881 for 24 hrs) and 22Rv1 (+/- 1 nM R1881 for 24 hrs) (obtained from the American Type Culture Collection). All cells were either stimulated or not stimulated with the synthetic androgen R1881 (1 or 10 nM for 24 or 48 hrs) prior to lysis (Qiagen miRNeasy minikit lysis buffer) and total RNA purification and DNase treatment.

2017-02-09 | GSE71797 | GEO

RNA-sequencing of LNCaP prostate cancer cells with and without treatment of enzalutamide

Project description:LNCaP prostate cancer cells were stimulated with the synthetic androgen R1881. RNA-sequencing was performed to identify changes induced by enzalutamide treatment on the transcriptome level.

2023-02-15 | GSE220097 | GEO

Long-term androgen withdrawal and treatment (R1881) of LNCaP-FGC prostate cancer cells

2013-10-22 | GSE51460 | GEO

Long-term androgen withdrawal and treatment (R1881) of LNCaP-FGC prostate cancer cells

Project description:LNCaP cells were cultures in steroid depleted medium for 5 days before treatment with synthetic androgen (R1881, 10nM) for 16h. Transcriptomics analysis was performed to compare gene expression changes induced by androgen withdrawal or androgen treatment. Genome-wide transcriptomic analysis of LNCaP cells grown in steroid depleted medium, normal (steroid-containing) medium and R1881 treated cells was performed using the Agilent platform

2013-10-22 | E-GEOD-51460 | biostudies-arrayexpress

Identification of direct androgen-target genes in the prostate cancer cell line LNCaP

Project description:Transcriptional profiling of the LNCaP cell line treated with R1881 synthetic androgen and/or cycloheximide. LNCaP cells were stimulated with R1881 alone, with cycloheximide alone, or with R1881 in the presence of cycloheximide for 24h and compared to control untreated cells. Two independent cell culture experiments for each treatment condition were performed for microarray analysis. Each experiment was repeated with a switch in fluorescent Cy3/Cy5 labels to account for dye effects to produce four data points per hybridization spot.

2014-06-14 | E-GEOD-22372 | biostudies-arrayexpress

Chromatin Accessibility Reveals Insight into Androgen Receptor Activation and Transcriptional Specificity

Project description:Using DNase-seq, mRNA-seq and publicly available ChIP-seq data sets, we examined the role of chromatin accessibility (DNase-seq) in androgen receptor binding to the genome (ChIP-seq) and AR-mediated transcriptional changes (mRNA-seq). Our data reveals genome-wide changes in chromatin structure that correspond to AR binding and differential gene expression. A focused examination of DNase-seq data around androgen receptor motifs within androgen receptor ChIP-seq peaks reveals distinct patterns of protection from DNaseI cleavage. Examination of chromatin accessibility (DNase-seq), AR binding (AR ChIP-seq), and transcription (mRNA-seq) in LNCaP cells before and after 12 hours of 1 nM R1881 treatment This Series represents the RNA-Seq data only. Exon microarray data generated under the same conditions is available through GSE15805. The DNase-seq data is publicly available through GSE32970 as well as the UCSC genome browser (genome.ucsc.edu) under Regulation::ENCODE DNase/FAIRE::Duke DNaseI HS:LNCaP and LNCaP + Andro. The accession numbers for the ChIP-seq experiments used are GSE14097 and GSE28126.

2012-08-14 | E-GEOD-34780 | biostudies-arrayexpress

Identification of direct androgen-target genes in the prostate cancer cell line LNCaP

Project description:Transcriptional profiling of the LNCaP cell line treated with R1881 synthetic androgen and/or cycloheximide.

2014-06-14 | GSE22372 | GEO

Prostasphere-forming cells of human prostate cancer cell LNCaP: Control vs. Hormone treated

Project description:Transcriptional profiling of LNCaP prostasphere-forming cells, comparing control untreated sphere-forming cells with hormone treated sphere-forming cells. Both estrogen (estradiol) and androgen (R1881) promote the sphere formation of human prostate cancer cell LNCaP. Goal was to determine the effects of hormones on global gene expression of LNCaP sphere-forming cells. Five samples were analyzed. Control (ethanol 1hr), estradiol 1 hour, estradiol 24 hour, R1881 1 hour, R1881 24 hour.

2012-04-23 | E-GEOD-37531 | biostudies-arrayexpress

Duke DNase-seq in LNCaP

Project description:Duke DNase-seq in LNCaP

| PRJNA661448 | ENA

Gene expression of LNCaP cells grown in polyethlene glycol-based hydrogels alone (monocultures) and grown with human osteoblasts as tissue engineered bone (co-culture) with the presence of synthetic androgen, R1881

Project description:Analysis of LNCaP cell molecular differences in monocultures and in co-cultures in the presence of R1881. Human osteoblast molecular signatures were also identified from the tissue engineered bone monocultures. LNCaP cells molecular profile was altered by co-culturing with human osteoblasts compared to LNCaP monocultures with or without R1881 stimulations. These results provide insights into the behavioral change of LNCaP cells in a bone-like microenvironment.

2014-05-13 | GSE44143 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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