Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

ABSTRACT: Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

PROVIDER: PRJNA533284 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10956413.fastq.gz	Fastqsanger.gz
	SRR10956414.fastq.gz	Fastqsanger.gz
	SRR10956415.fastq.gz	Fastqsanger.gz
	SRR10956416.fastq.gz	Fastqsanger.gz
	SRR10956417.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

Project description:Aberrant expression of HOXC6 and HOXC4 is commonly detected in prostate cancer. The high expression of these transcription factors is associated with aggressive prostate cancer and can predict cancer recurrence after treatment. Thus, HOXC4 and HOXC6 are clinically relevant biomarkers of aggressive prostate cancer. However, the molecular mechanisms by which these HOXC genes contribute to prostate cancer is not yet understood. To begin to address the role of HOXC4 and HOXC6 in prostate cancer, we performed RNA-seq analyses before and after siRNA-mediated knockdown of HOXC4 and/or HOXC6 and also performed ChIP-seq to identify genomic binding sites for both of these transcription factors. Our studies demonstrate that HOXC4 and HOXC6 co-localize with HOXB13, FOXA1 and AR, three transcription factors previously shown to contribute to the development of prostate cancer. We suggest that the aberrantly upregulated HOXC4 and HOXC6 proteins may compete with HOXB13 for binding sites, thus altering the prostate transcriptome. This competition model may be applicable to many different human cancers that display increased expression of a HOX transcription factor.

2020-01-22 | GSE129951 | GEO

siRNA profiling of human LNCaP cells overexpressing/knockdown of HOXC6

Project description:The transcription factor HOXC6 is upregulated in human prostate cancer. SiRNA knockdown of HOXC6 induces apoptosis in LNCaP cells while upregulation rescued LNCaP cells from siRNA-induced apoptosis. We used microarrays to identify the genes whose expression underly the anti-apoptotic and proliferative effects of HOXC6 in LNCaP cells. Experiment Overall Design: LNCaP cells were transiently transfected with a cocktail of 5 siRNAs to HOXC6 to a final concentration of 100nM, with a HOXC6 gene expression vector, or control siRNA and vector. Cells were collected a 48hours post-transfection

2008-10-20 | E-GEOD-9182 | biostudies-arrayexpress

Genome wide mapping of PSF binding sites in prostate cancer cells

Project description:Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated long non-coding RNA, CTBP1-AS, located in the antisese region of CTBP1 gene. CTBP1-AS activate AR signaling by epigenetically repress AR-associated cofactors such as CTBP1 by interactign with RNA-binding protein PSF and recruiting HDAC complex to the target promoters. In order investigated the PSF target genes, we performed ChIP-seq analysis of PSF binding sites in prostate cancer cell line, LNCaP cells. We identified androgen dependent PSF binding regions in prostate cancer cell genome. We observed PSF bindings around the promoters of androgen repressed genes such as CTBP1, p53 and SMAD3. ChIP-sequence analysis of PSF binding sites in prostate cancer cells

2014-01-01 | E-GEOD-45124 | biostudies-arrayexpress

HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells

Project description:HOXC6 is a member of the HOX family, and its aberrant expression has been verified in a variety of cancers, such as prostate, breast,nasopharyngeal carcinoma,gastric, and ovarian cancers.Some studies suggest that HOXC6 might be involved in tumor initiation and progression.However, the role of HOXC6 in esophageal squamous cell carcinoma cells has not been fully investigated.Here we study how HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells

2019-02-22 | GSE121976 | GEO

Expression data from overexpression and knockdown of HOXC6 in LNCaP cells

2008-07-01 | GSE9182 | GEO

Gene expression-based, HOXC6 WT versus KO mouse prostates

Project description:This study was used to identify biologically relevant targets of HOXC6 in normal prostate. Keywords: gene expression profiling

2008-03-01 | GSE9207 | GEO

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells.

| S-EPMC6996832 | biostudies-literature

Genome wide mapping of PSF binding sites in prostate cancer cells

2014-01-01 | GSE45124 | GEO

Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HOXC6-HA/YFP

Project description:The transcription factor HOXC6 is upregulated in human prostate cancer. SiRNA knockdown of HOXC6 induces apoptosis in LNCaP cells while upregulation rescued LNCaP cells from siRNA-induced apoptosis. We used chromatin immunoprecipitaiton followed by microarray to identify the gene promoters that are bound by HOXC6 in LNCaP cells. Keywords: Stable expression and chromatin immunoprecipitation

2008-03-01 | GSE9772 | GEO

Genome wide VDR binding sites in RWPE1 human prostate epithelial cells

Project description:Signaling through the vitamin D receptor (VDR) has been proposed to suppress the development of epithelial cancers, including prostate cancer. We conducted ChIP-seq to identify the VDR binding sites in the genome of the prostate epithelial cell line, RWPE1. This analysis reveals a large number of VDR binding sites in both control cells and in cells treated with 10 nM 1,25 dihydroxyvitamin D3 for 3 hours. These peaks are associated with genes controlling a wide variety of cellular functions.

2019-04-10 | GSE116843 | 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