ONTOLOGY SOURCE REFERENCE Term Source Name "CHEBI" "EFO" "CLO" "NCBITAXON" "PATO" "MP" "XCO" "UO" Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/EFO" "http://data.bioontology.org/ontologies/CLO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/MP" "http://data.bioontology.org/ontologies/XCO" "http://data.bioontology.org/ontologies/UO" Term Source Version "78" "111" "39" "2" "160" "273" "33" "42" Term Source Description "Chemical Entities of Biological Interest Ontology" "Experimental Factor Ontology" "Cell Line Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Phenotypic Quality Ontology" "Mammalian Phenotype Ontology" "Experimental Conditions Ontology" "Units of Measurement Ontology" INVESTIGATION Investigation Identifier "" Investigation Title "" Investigation Description "" Investigation Submission Date "" Investigation Public Release Date "" Comment [Created with configuration] "" Comment [Last Opened With Configuration] "" Comment[Created With Configuration] "" Comment[Last Opened With Configuration] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "" Investigation Publication DOI "" Investigation Publication Author List "" Investigation Publication Title "" Investigation Publication Status "" Investigation Publication Status Term Accession Number "" Investigation Publication Status Term Source REF "" INVESTIGATION CONTACTS Investigation Person Last Name "" Investigation Person First Name "" Investigation Person Mid Initials "" Investigation Person Email "" Investigation Person Phone "" Investigation Person Fax "" Investigation Person Address "" Investigation Person Affiliation "" Investigation Person Roles "" Investigation Person Roles Term Accession Number "" Investigation Person Roles Term Source REF "" STUDY Study Identifier "E-GEOD-34112" Study Title "Transcriptional profiling of PC3 prostate cancer cells treated with the NSAIDs sulindac or nitrosulindac (aka NO-sulindac, NCX-1102). [original title: Effect of NO-sulindac treatment on hypoxic prostate cancer cells]" Study Description "Cells were grown either in hypoxic or normoxic conditions and treated either with NSAID (sulindac or nitrosulindac) or control media (DMSO only or no drug). [original description: The hypoxia response contributes to radio and chemo-resistance in cancer cells. Our previous work has shown that the nitric oxide donating non-steroidal anti-inflammatory drug (NO-NSAID) NO-sulindac is a potent inhibitor of the hypoxia response in prostate cancer cells and leads to increased susceptibility to radiation. In this study we used microarrays to investigated the global impact of NO-sulindac on the hypoxia response in prostate cancer cells with a view to determining the mechanism of action. PC3 hormone-insensitive prostate cancer cells were grown under normoxic or hypoxic conditions and treated with NO-sulindac, unnitrated sulindac or vehicle control. Global gene expression in response to treatment was examined using microarrays and the bioconductor software suite. Gene set enrichment analysis (GSEA), Gene ontology (GO) analysis and pathway analysis were used to examine the biological impact of treatments.]" Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "" Study Public Release Date "2012-12-01" Study File Name "s_E-GEOD-34112_study_samples.txt" STUDY DESIGN DESCRIPTORS Study Design Type "transcription profiling by array" Study Design Type Term Accession Number "" Study Design Type Term Source REF "" STUDY PUBLICATIONS Study PubMed ID "" Study Publication DOI "" Study Publication Author List "" Study Publication Title "" Study Publication Status "" Study Publication Status Term Accession Number "" Study Publication Status Term Source REF "" STUDY FACTORS Study Factor Name "treatment" "oxygen level" "environmental condition" "oxygen level description" "NSAID concentration" Study Factor Type "treatment" "oxygen level" "environmental condition" "oxygen level description" "concentration" Study Factor Type Term Accession Number "" "" "" "" "" Study Factor Type Term Source REF "" "" "" "" "" STUDY ASSAYS Study Assay File Name "a_E-GEOD-34112_GeneChip_assay.txt" Study Assay Measurement Type "transcription profiling" Study Assay Measurement Type Term Accession Number "" Study Assay Measurement Type Term Source REF "" Study Assay Technology Type "DNA microarray" Study Assay Technology Type Term Accession Number "" Study Assay Technology Type Term Source REF "" Study Assay Technology Platform "" STUDY PROTOCOLS Study Protocol Name "P-GSE34112-3" "P-GSE34112-2" "P-GSE34112-4" "P-GSE34112-5" "P-GSE34112-6" "P-GSE34112-7" "P-GSE34112-8" "P-GSE34112-1" Study Protocol Type "grow" "specified_biomaterial_action" "nucleic_acid_extraction" "labeling" "hybridization" "image_aquisition" "feature_extraction" "bioassay_data_transformation" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "" "" "" "" Study Protocol Description "PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100 U/ml, streptomycin 100 µg/ml (all from Invitrogen, Paisley, UK)." "On Day 0, PC-3 cells were seeded at 2x10^6 cells/25cm^2 flask and left overnight in a 37°C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma-Aldrich, Gillingham, UK), 25 µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25 µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37°C, 5% CO2) or in hypoxic conditions (0.2% O2, 37°C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs." "After 48 hours incubation 700 µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5 ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK)." "For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100 ng of total RNA was reverse transcribed per the manufacturer's protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75 µg of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array" "Labelled cDNA was hybridized to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc." "Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer" "The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA." "ID_REF = VALUE = RMA normalized data on the log2 scale" Study Protocol URI "" "" "" "" "" "" "" "" Study Protocol Version "" "" "" "" "" "" "" "" Study Protocol Parameters Name "" "" "" "" "" "" "" "" Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" "" Study Protocol Components Name "" "" "" "" "" "" "" "" Study Protocol Components Type "" "" "" "" "" "" "" "" Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" "" STUDY CONTACTS Study Person Last Name "Gallagher" "Gallagher" Study Person First Name "Iain" "Iain" Study Person Mid Initials "" "J" Study Person Email "iain.gallagher@ed.ac.uk" "" Study Person Phone "00 44 131 242 6523" "" Study Person Fax "" "" Study Person Address "Tissue Injury & Repair, Edinburgh University, The Chancellor's Building, 49 Little France Crescent, Edinburgh, United Kingdom" "" Study Person Affiliation "Edinburgh University" "" Study Person Roles "submitter" "" Study Person Roles Term Accession Number "" "" Study Person Roles Term Source REF "" "" Comment[Study Person REF] "" ""