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E-GEOD-15266 - Effects of far-infrared rays on prostate cancer cells and normal prostate epithelial cells

Status
Submitted on 17 March 2009, released on 5 June 2010, last updated on 1 May 2014
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (9)
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.
Experiment type
transcription profiling by array 
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-15266.idf.txt
Sample and data relationshipE-GEOD-15266.sdrf.txt
Raw data (1)E-GEOD-15266.raw.1.zip
Processed data (1)E-GEOD-15266.processed.1.zip
Array designA-GEOD-8312.adf.txt
Links