ONTOLOGY SOURCE REFERENCE
Term Source Name	"EFO"	"CLO"	"BTO"	"CHEBI"	"UO"	"NCBITaxon"	
Term Source File	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/50454"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO"	"http://bioportal.bioontology.org/ontologies/50447"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UO"	"http://bioportal.bioontology.org/ontologies/47845"	
Term Source Version	""	"50454"	"Jun 2010"	"50447"	"Jun 2010"	"47845"	
Term Source Description	""	"Cell Line Ontology"	"BRENDA tissue / enzyme source"	"Chemical Entities of Biological Interest Ontology"	"Unit Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	
INVESTIGATION
Investigation Identifier	""
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Comment [Last Opened With Configuration]	""
INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-22445"
Study Title	"Mesothelioma cells treated with the NSAID piroxicam and/or the anticancer drug cisplatin [original title: Apoptosis induced by Piroxicam/Cisplatin combined treatment is triggered by p21 in mesothelioma]"
Study Description	"Here we report that piroxicam/cisplatin combined treatment exerts an apoptotic effect on mesothelioma cells. Genome-wide transcriptome analyses lead us to identify p21 as the possible apoptosis mediator acting as downstream target of the piroxicam/cisplatin treatment. To analyze the potential therapeutic effect of the piroxicam/cisplatin treatment at molecular level, and to identify gene expression pattern modifications following the combined treatment, we performed a transcriptional profiling on HGU133A arrays, using cells treated with piroxicam, cisplatin or with piroxicam and cisplatin, choosing the time exposures in which apoptosis induction was absent or evident (8 and 24 hours). Biological duplicates or triplicates were generated for each prototypic situation and data were analyzed using the oneChannelGUI Bioconductor package (Sanges et al., 2007), comparing untreated cells with cells treated in single or combined treatment. After quality controls, the complexity of the data set was reduced removing the non-significant probe sets, resulting in a total of 4,247 out of the 22,283 probe sets present in the microarray. To assess differential expression, linked to piroxicam, cisplatin- and the combined treatment we used an empirical Bayes method together with a false discovery rate (FDR) correction of the P-value. Specifically genes were selected using a corrected p-value ≤0.05 and |log2(fc)| ≥1. We detect a total of 536 differentially expressed genes."
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2011-11-20"
Study File Name	"s_E-GEOD-22445_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
Study Design Type Term Accession Number	""
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STUDY PUBLICATIONS
Study PubMed ID	"21858171"
Study Publication DOI	"10.1371/journal.pone.0023569"
Study Publication Author List	"Baldi A, Piccolo MT, Boccellino MR, Donizetti A, Cardillo I, La Porta R, Quagliuolo L, Spugnini EP, Cordero F, Citro G, Menegozzo M, Calogero RA, Crispi S"
Study Publication Title	"Apoptosis induced by piroxicam plus cisplatin combined treatment is triggered by p21 in mesothelioma."
Study Publication Status	""
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"time"	"other drug"	"NSAID"
Study Factor Type	"time"	"chemical compound"	"chemical compound"
Study Factor Type Term Accession Number	""	"obo:CHEBI_37577"	"obo:CHEBI_37577"
Study Factor Type Term Source REF	""	"EFO"	"EFO"
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-22445_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	""
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Study Assay Technology Type	"DNA microarray"
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Study Assay Technology Platform	""
STUDY PROTOCOLS
Study Protocol Name	"P-GSE22445-1"	"P-GSE22445-6"	"P-GSE22445-3"	"P-GSE22445-8"	"P-GSE22445-7"	"P-GSE22445-2"	"P-GSE22445-4"	"P-GSE22445-5"
Study Protocol Type	"bioassay_data_transformation"	"hybridization"	"grow"	"feature_extraction"	"image_aquisition"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"
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Study Protocol Description	"ID_REF = <br>VALUE = log2-GCRMA"	"Hybridization was done using Affymetrix kit and following manufacturer indications"	"Cells were cultured as monolayers in flasks using American Type Culture Collection complete growth medium in a humidified atmosphere containing 5% CO2 at 37¡C."	"Microarray quality control and statistical validation were performed using oneChannelGUI Bioconductor package. Intensity summarization was done with GCRMA and quantile normalization"	"Scanner procedures were done using a Genechip Affymetrix station (FS 450, Scanner 3000) following manufacturer indications"	"Drug treatments: Cells were seeded in complete growth medium 16 hours before the experiments, in order to allow attachment but not cell-doubling. Then cells were treated with piroxicam (760 microM) and cisplatin (4.5 microg/mL) alone or in combination for 8 or 24 hours. Control samples were untreated."	"Total RNA was extracted and purified using the RNeasy Midi kit (Qiagen, Valencia, CA, USA)"	"Biotinylated cRNA target preparation was done using Affymetrix kit and following manufacturer indications"
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STUDY CONTACTS
Study Person Last Name	"Calogero"	"BALDI"	"BOCCELLINO"	"DONIZETTI"	"LAPORTA"	"SPUGNINI"	"CARDILLO"	"CITRO"	"QUAGLIUOLO"	"MENEGOZZO"	"CORDERO"	"CALOGERO"	"CRISPI"
Study Person First Name	"Raffaele"	"ALFONSO"	"MARIAROSARIA"	"ALDO"	"RAFFAELE"	"ENRICO"	"IRENE"	"GENNARO"	"LUCIO"	"MASSIMO"	"FRANCESCA"	"RAFFAELE"	"STEFANIA"
Study Person Mid Initials	"A"	""	""	""	""	"P"	""	""	""	""	""	"A"	""
Study Person Email	"raffaele.calogero@unito.it"	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Phone	"++39 0116706457"	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Fax	"++39 0119038639"	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Address	"Molecular Biotechnology Center, University of Torino, Via Nizza 52, Torino, To, Italy"	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Affiliation	"University of Torino"	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""	""	""	""	""	""
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Comment[Study Person REF]	""	""	""	""	""	""	""	""	""	""	""	""	""