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Identification of ZBTB7A cistrome and transcriptome profiles in VCaP prostate cancer cells

ABSTRACT: Identification of ZBTB7A cistrome and transcriptome profiles in VCaP prostate cancer cells

PROVIDER: PRJNA507613 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8259110.fastq.gz	Fastqsanger.gz
	SRR8259102.fastq.gz	Fastqsanger.gz
	SRR8259103.fastq.gz	Fastqsanger.gz
	SRR8259104.fastq.gz	Fastqsanger.gz
	SRR8259105.fastq.gz	Fastqsanger.gz

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ZBTB7A ChIP-seq under different DHT level

Project description:Zinc finger and BTB domain containing transcription repressor ZBTB7A has been recently reported as a tumor suppressor who plays important functions to prevent the progression of prostate cancer. However, the chromatin activity of ZBTB7A in prostate cancer cells remain unclear. In order to identify the cistrome and transcriptome of ZBTB7A, we performed ZBTB7A ChIP-seq in VCaP cells and RNA-seq in VCaP cells transfected with siRNA targeting ZBTB7A or non-targeting control, respectively (cells were grown in full serum). By using combined ChIP-seq and RNA-seq analyses in VCaP cells, we have precisely mapped the ZBTB7A binding sites and identified a subset of genes that are directly repressed by ZBTB7A. To study the chromatin interaction of ZBTB7A with androgen receptor (AR), we also performed ChIP-seq of ZBTB7A in VCaP cells stimulated with 10 nM DHT for 4 hours versus vehicle control (cells were hormone-depleted prior to DHT stimulation). Our results show that ZBTB7A binding is increased by androgen at AR and ZBTB7A overlapping sites.

2019-09-12 | GSE123089 | GEO

RNA-seq with knockdown ZBTB7A and NTC control

2019-09-12 | GSE123090 | GEO

Identification of ZBTB7A cistrome and transcriptome profiles in VCaP prostate cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-09-12 | GSE123091 | GEO

Dexamethasone treatment of VCaP prostate cells

Project description:The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide. We identified glucocorticoid receptor (GR) activity as modulator of enzalutamite sensitivity in the VCaP prostate cancer cell line. The GR agonist dexamethasone was sufficient to confer enzalutamide resistance whereas a GR antagonist restored sensitivity. These expression profiling data demonstrate that GR transcriptional activity overlaps with that of AR in the VCAP model.

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Dexamethasone treatment of VCaP prostate cells

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AR binding in prostate cancer cell lines VCaP and VCS2

Project description:This SuperSeries is composed of the following subset Series: GSE32344: Expression profilling of prostate cancer VCaP and VCS2 cells GSE32345: Genome-wide maps of AR binding in prostate cancer cell lines VCaP and VCS2 Refer to individual Series

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ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes

Project description:Libraries of single-stranded oligodeoxynucleotides (ssODNs) can be enriched for sequences that specifically bind molecules on naïve complex biological samples like cells or tissues. Depending on the enrichment strategy, the ssODNs can identify molecules specifically associated with a defined biological condition, for example a pathological phenotype, and thus are potentially useful for biomarker discovery. We performed ADAPT, a variant of SELEX, on exosomes secreted by VCaP prostate cancer cells. A library of ~1011 ssODNs was enriched for those that bind to VCaP exosomes and discriminate them from exosomes derived from LNCaP prostate cancer cells. Next-generation sequencing (NGS) identified the best discriminating ssODNs, nine of which were resynthesized and their discriminatory ability confirmed by qPCR. Affinity purification with one of the sequences (Sequence 7) combined with LC-MS/MS identified its molecular target complex, whereof most proteins are part of or associated with the multiprotein ESCRT complex participating in exosome biogenesis. Within this complex, YBX1 was identified as the directly bound target protein. ADAPT thus is able to differentiate exosomes from cancer cell subtypes from the same lineage. The composition of ESCRT complexes in exosomes from VCaP versus LNCaP cells might constitute a discriminatory element between these prostate cancer subtypes.

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Expression profiling of human prostate VCaP and LNCaP cancer cells after silencing ERG or ETV1, respectively

Project description:Chromosomal rearrangements involving ETS factors, ERG and ETV1, occur frequently in prostate cancer. We here examine human prostate cancer cells control VCaP and LNCaP cells with ERG- or ETV1-silenced VCaP or LNCaP cells, respectively, in hormone deprived and stimulated conditions.

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Identification of NEDD9 regulated genes in VCaP prostate cancer cells

Project description:Identification of NEDD9 regulated genes in VCaP prostate cancer cells

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Gene expression profiles of Vcap xenograft tumors with chemical or physical denervation.

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