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An analysis of the changes in miRNA expression induced by AR, HOXC6 or NKX2-2 overexpression via Next-generation sequencing

ABSTRACT: The goal of this study is to validate that AR, HOXC6 and NKX2-2 co-regulate the same core set of metastasis associated miRNAs in prostate cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE71081 | GEO | 2017/06/13

SECONDARY ACCESSION(S): PRJNA290322

REPOSITORIES: GEO

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mRNA expression analysis of AR, HOXC6 and NKX2-2 overexpression

Project description:Investigation of mRNA expression level changes in RWPE1 cells with AR,HOXC6 and NKX2-2 overexpression. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

2017-06-13 | GSE81232 | GEO

Expression data from overexpression and knockdown of HOXC6 in LNCaP cells

2008-07-01 | GSE9182 | 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 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

Next Generation Sequencing Analysis of Wild Type and Hypomorphic Nkx2-5 mutant heart Transcriptomes

Project description:We report the transcriptome analysis of E11.5 mouse embryonic heart presenting a reduction in Nkx2-5 expression compare to wild-type littermate. Transcriptome analysis of 3 different E11.5 hypomorphic hearts against 3 controls littermate hearts.

2015-09-02 | E-GEOD-44573 | biostudies-arrayexpress

Homo sapiens

Project description:mRNA expression analysis of AR, HOXC6 and NKX2-2 overexpression

| PRJNA321025 | ENA

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

Next Generation Sequencing Analysis of Wild Type and Hypomorphic Nkx2-5 mutant heart Transcriptomes

Project description:We report the transcriptome analysis of E11.5 mouse embryonic heart presenting a reduction in Nkx2-5 expression compare to wild-type littermate.

2015-09-02 | GSE44573 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of effect of knockdown of GATA2 on AR binding sites

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2. Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding. Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer. LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.

2014-01-21 | E-GEOD-52725 | biostudies-arrayexpress

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

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