Unknown,Transcriptomics,Genomics,Proteomics

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Microarray Analysis of DU 145, LNCaP and PC-3 Prostate Cancer Cell Lines upon Docetaxel treatment

ABSTRACT: We measured the effect of docetaxel treatment to three differentially responsive prostate cancer cell lines, LNCaP, DU145 and PC-3, based on a transcriptional time course response by microarray analysis. These cell lines represent both androgen independent (DU145 and PC-3) and androgen sensitive (LNCaP) cells Hybridized arrays were scanned with Agilentâs dual laser-based scanner. Feature Extraction software version 10.5 (Agilent Technologies) was used to link a feature to a design file and to determine the relative fluorescence intensity between two samples. Dye swap strategy with alternate cy3 and cy5 labeling on docetaxel treated and control groups over four time points was used to have technical replicates and decrease dye bias.

ORGANISM(S): Homo sapiens

SUBMITTER: Robert Moritz

PROVIDER: E-GEOD-83654 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This SuperSeries is composed of the following subset Series: GSE15259: The effects of far-infrared rays on normal prostate epithelial cells (PrEC) GSE15260: Effects of far-infrared rays on 3 human prostate cancer cell lines GSE16077: Effects of far-infrared rays on human prostate cancer cell line PC-3 FIR stands for far-infrared rays that was reflected and radiated from RB. Refer to individual Series RNA was extracted with Isogen kit (NIPPON GENE CO., LTD. Osaka, Japan) from PrECs, and PC-3 with or without exposure to FIR on the 7th and 12th day of culture. Aliquots of 200 ng of total RNAs were labeled with Cy3- or Cy5- UTP using Agilent Quick Amp Labeling Kit (Agilent Technologies Inc, Tokyo, Japan) according to the manufacturer instructions. The Cy3-labeled probe using RNA from cells treated with DMSO and the Cy5-labeled probe using RNA from cells treated with DNCB for 4.5 hr were mixed, fragmented, and then suspended in GE hybridization buffer in the Gene Expression Hybridization Kit (Agilent Technologies Inc, Tokyo, Japan). The probes were applied to Whole Human Genome Oligo array (Agilent Technologies Inc, Tokyo, Japan), and hybridization, washing, and scanning by Agilent Microarray Scanner were performed according to the manufacturer $B!G (Bs recommended protocol. The images were processed using Feature Extraction Software (ver9.5.3.1, Agilent). For each hybridized spot, background intensity was subtracted and normalized by the global LOWESS normalization method. Dye-swap was performed. More than 2 fold and less than 0.5 fold changes are assigned positive on data analysis. RNA extracted from FIR-treated and non-FIR treated DU145, PC3, and LNCaP on the 21st and 28th day of culture were also treated in the same way except the use of commercially available IntelliGene HS Human Expression chip (TAKARA BIO, Otsu, Japan). Data analysis was performed using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland). Functional analyses were performed and the networks were generated using Ingenuity Pathways Analysis (Ingenuity Systems, CA, USA) cDNA microarray. BRCA1 and associated genes for DNA repair were significantly up-regulated in PrECs on the 7th day, and PC-3 on the 12th day when they were exposed to FIR (Fig. 2). These up-regulated genes were all normalized on the 12th day in PrECs, and there were no significant up-regulation of DNA repair pathway by FIR in DU145 and LNCaP on the 7th and 12th day.