ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"NCBITAXON"	"UO"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/UO"	
Term Source Version	"78"	"111"	"20"	"2"	"42"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Units of Measurement Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-12112"
Study Title	"Sprague-Dawley rats treated with celecoxib to prevent induced cancer. [original title: Chemoprevention of the hepatocarcinogenesis by celecoxib]"
Study Description	"Male rats were treated with diethylnitrosamine and 2-acetylaminofluorene to induce cancer. 4 rats were fed celecoxib throughout, starting 1 week before induction; 4 rats were fed celecoxib starting 18 days after induction, and 4 rats were not given celecoxib. After 25 days, livers were harvested and subjected to transcriptional profiling. [original (edited) description: Microarray analysis is a useful methodology to identify target genes modulated by anticancer drugs. Here, celecoxib['s] effect on gene expression profiles was evaluated in the modified resistant hepatocyte model. Animals subjected to carcinogenic treatment were fed [a] diet containing 1500 ppm of celecoxib. Two schemes of celecoxib administration were designed. In the progression protocol, celecoxib was administrated between days 18 and 25 post-cancer initiation, [for] a total of 8 celecoxib treatment days, when well established preneoplastic lesions start to appear. In the initiation protocol, celecoxib was administrated from one week before until 25 days after ... cancer initiation, [for] a total of 32 celecoxib treatment days. A rat group was subjected only to the carcinogenic treatment as cancer positive control. Gene expression profiles of all groups were compared to a negative untreated control. The evaluation of gene expression profiles permitted us to identify new target genes that are modulated by celecoxib treatment. A possible mechanism of celecoxib chemoprevention of hepatocarcinogenesis is proposed. 9-week-old Sprague-Dawley rats, 4 rats per group, were subjected to Semple-Roberts' modified hepatocarcinogenesis protocol and sacrificed 25 days post-initiation. In celecoxib-treated groups, celecoxib was administrated mixed in diet at 1500 ppm. Negative and positive cancer progression controls were included to compare gene expression profiles. Microarray analysis was performed on liver samples, one replicate per rat, using dye swap.]"
Comment[Study Grant Number]	""
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Study Submission Date	""
Study Public Release Date	"2009-07-10"
Study File Name	"s_E-GEOD-12112_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"20145537"
Study Publication DOI	""
Study Publication Author List	"Arellanes-Robledo J, Salcido-Neyoy ME, Márquez-Quiñones A, García-Román R, Beltrán-Ramírez O, Le Berre V, Sokol S, François JM, Villa-Treviño S"
Study Publication Title	"Celecoxib activates Stat5 and restores or increases the expression of growth hormone-regulated genes in hepatocarcinogenesis."
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STUDY FACTORS
Study Factor Name	"treatment"
Study Factor Type	"treatment"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-12112_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE12112-5"	"carcinogenic treatment"	"initiation"	"progression"	"P-GSE12112-17"	"P-GSE12112-6"	"P-GSE12112-7"	"P-GSE12112-10"	"P-GSE12112-14"	"P-GSE12112-16"	"P-GSE12112-11"	"P-GSE12112-13"	"P-GSE12112-12"	"P-GSE12112-2"	"P-GSE12112-1"	"P-GSE12112-3"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"labeling"	"labeling"	"labeling"	"hybridization"	"feature_extraction"	"image_acquisition"	"bioassay_data_transformation"	"bioassay_data_transformation"	"bioassay_data_transformation"
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Study Protocol Description	"Under Institutional Animal Care and Use Committee Guidelines, animals were fed ad libitum with 5001 diet and housed in a controlled environment with a 12-h light/dark cycle and a temperature of 23°C until sacrifice."	"Six-week-old rats were injected intraperitoneally with diethylnitrosamine (200 mg/kg body weight).  Seven days later, 2-acetylaminofluorene (20 mg/kg) was administered orally for 3 consecutive days.  Livers were harvested at 25 days post-injection (age ~ 9.5 weeks)."	"Starting a week before administration of diethylnitrosamine, celecoxib (1500 ppm) was added to the animals' diet.  Celecoxib administration continued until livers were harvested at 25 days post-injection (age ~ 9.5 weeks)."	"Starting 18 days after administration of diethylnitrosamine, celecoxib (1500 ppm) was added to the animals' diet.  Celecoxib administration continued until livers were harvested at 25 days post-injection (age ~ 9.5 weeks)."	"Carcinogenic treatment, the rats were initiated with an intraperitoneal injection of 200 mg/kg of body weight of diethylnitrosamine and 7 days later, 2-acetylaminofluorene was orally administered at 20 mg/kg doses for 3 consecutive days before partial hepatectomy, starting from 6 weeks old until sacrifice at 25 days post-hepatocarcinogenesis initiation. Celecoxib was administrated at 1500 ppm mixed in the 5001 diet. The administration was given since a week before until 25 days after of cancer initiation, a total of 32 days of treatment."	"Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNAlater and stored at -80°C. Isolation of total RNA from liver samples was following the instructions for Qiagen Rneasy mini kit. Quality and quantity were determined by capillary electrophoresis (RNA 6000 nano assay, Agilent)."	"Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm."	"Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm."	"Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm."	"Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm."	"8h at 42°C in the automatic hybridization machine discovery from Ventana. After hybridization, slides were washed twice in Ribowash buffer for 5 minutes with agitation and then once with 0.1xSSC buffer."	"Background subtraction with lowess allowed value 10, log transformation and LOWESS normalization."	"Scanning with Genepix 400A microarray scanner (Axon instruments). Image analysis was made by Genepix Pro V6 software, each spot was evaluated and selectioned to be analyzed by Bioplot software."	"ID_REF = <br>CH1_SIG_MEAN = Raw Intensity from Carcinogen and Celecoxib in initiation protocol<br>CH1_BKD_MEAN = Raw Background from carcinogen and celecoxib in initiation protocol<br>CH2_SIG_MEAN = Raw Intensity from normal rats<br>CH2_BKD_MEAN = Raw Background from normal rats<br>VALUE = Normalized ratio channel 1/channel 2"	"ID_REF = <br>CH1_SIG_MEAN = Raw Intensity from Carcinogen-treated rats<br>CH1_BKD_MEAN = Raw Background from carcinogen-treated rats<br>CH2_SIG_MEAN = Raw Intensity from normal rats<br>CH2_BKD_MEAN = Raw Background normal rats<br>VALUE = Normalized ratio channel 1/channel 2"	"ID_REF = <br>CH1_SIG_MEAN = Raw Intensity from Carcinogen and Celecoxib in progression protocol<br>CH1_BKD_MEAN = Raw Background from carcinogen and celecoxib in progression protocol<br>CH2_SIG_MEAN = Raw Intensity from normal rats<br>CH2_BKD_MEAN = Raw Background from normal rats<br>VALUE = Normalized ratio channel 1/channel 2"
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STUDY CONTACTS
Study Person Last Name	"Marquez-Quiñones"	"Arellanes-Robledo"	"Salcido-Neyoy"	"Marquez-Quiñones"	"Garcia-Roman"	"Beltran-Ramirez"	"LeBerre"	"Sokol"	"François"	"Villa-Treviño"
Study Person First Name	"Adriana"	"Jaime"	"Martha"	"Adriana"	"Rebeca"	"Olga"	"Veronique"	"Serguei"	"Jean-Marie"	"Saul"
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Study Person Email	"addy_mq@yahoo.com"	""	""	""	""	""	""	""	""	""
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Study Person Address	"Cell Biology, CINVESTAV, AV. Instituto Politecnico Nacional No. 2508, Mexico, DF, MEXICO"	""	""	""	""	""	""	""	""	""
Study Person Affiliation	"CINVESTAV"	""	""	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""	""	""
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