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CCFAlmasan_CaP1

ABSTRACT: The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R). Keywords = Human Keywords = Prostate Keywords = Cancer Keywords = Adenocarcinoma Keywords = Ionizing Radiation Keywords = Microarray Keywords: ordered

ORGANISM(S): Homo sapiens

PROVIDER: GSE762 | GEO | 2004/06/01

SECONDARY ACCESSION(S): PRJNA87713

REPOSITORIES: GEO

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CCF_Almasan_CaPK

Project description:The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source. Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation. The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr. After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R). Keywords = Human Keywords = Prostate Keywords = Cancer Keywords = Adenocarcinoma Keywords = Ionizing Radiation Keywords = Microarray Keywords: time-course

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CCF_Almasan_CaPGSE56

Project description:The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function. Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source. Total RNA was extracted from cells at 6 and 24 hours after irradiation. The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr. It was not irradiated and was transfected with the base pLXSN retrovirus, lacking the inserted GSE56 coding region. After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R). Keywords = Human Keywords = Prostate Keywords = Cancer Keywords = Adenocarcinoma Keywords = Ionizing Radiation Keywords = Microarray Keywords = p53 Keywords = GSE56 Keywords: time-course

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Transcription profiling of human prostate adenocarcinoma cells

Project description:The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).

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Transcription profiling of human prostate carcinoma cell LNCaP C4-2 after gamma irradiation with 10 Sv

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived NGF-overexpressed LNCaP cells transcriptome profiling (RNA-seq) to microarray methods and to evaluate NGF signature for optimal high-throughput data analysis. Method: LNCaP/EV and LNCaP/NGF cells were cultured in RPMI 1640 medium supplemented with 10% FBS. An RNeasy Midi Kit (Qiagen, Redwood City, CA, USA) was used for total RNA isolation. The cDNA library was prepared by KAPA mRNA HyperPrep Kits (Roche) and sequenced using the NovaSeqTM 6000 sequencing system (Illumina, San Diego, CA, USA) in 300~400-bp paired-end reads. Results: Here we show that an androgen-deprivation therapy (ADT)-stimulated transcription factor, ZBTB46, upregulated NGF via ZBTB46 mediated-transcriptional activation of NGF. Our results reveal a role of the NGF in the development of NEPC that is linked to ZBTB46 upregulation. Conclusion: Our study provides evidence that the ZBTB46-NGF axis has potential to be considered as a therapeutic target to impair NEPC progression.

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