ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"NCBITAXON"	"ERO"	"XCO"	"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/ERO"	"http://data.bioontology.org/ontologies/XCO"	"http://data.bioontology.org/ontologies/UO"	
Term Source Version	"78"	"111"	"20"	"2"	"13"	"33"	"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"	"Eagle-I Research Resource Ontology"	"Experimental Conditions Ontology"	"Units of Measurement Ontology"	
INVESTIGATION
Investigation Identifier	""
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-16752"
Study Title	"Rat liver. Control vs. Chemical treated: time course"
Study Description	"This SuperSeries is composed of the following subset Series: GSE16340: Rat liver. Control vs. Chemical treated, 3 days GSE16394: Rat liver. Control vs. Chemical treated, 28 days GSE16743: Rat liver: Control vs. Chemical treated, 14 days Refer to individual Series"
Comment[Study Grant Number]	""
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Study Submission Date	""
Study Public Release Date	"2009-06-23"
Study File Name	"s_E-GEOD-16752_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"20011461"
Study Publication DOI	""
Study Publication Author List	"Matsumoto H, Yakabe Y, Saito K, Sumida K, Sekijima M, Nakayama K, Miyaura H, Saito F, Otsuka M, Shirai T."
Study Publication Title	"Discrimination of carcinogens by hepatic transcript profiling in rats following 28-day administration."
Study Publication Status	"Published"
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STUDY FACTORS
Study Factor Name	"compound"	"age"	"treatment"	"dose"	"vehicle"
Study Factor Type	"compound"	"age"	"treatment"	"dose"	"vehicle"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-16752_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-GSE16752-4"	"P-GSE16752-3"	"P-GSE16752-5"	"P-GSE16752-6"	"P-GSE16752-7"	"P-GSE16752-8"	"P-GSE16752-9"	"P-GSE16752-10"	"P-GSE16752-1"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"	"image_acquisition"	"feature_extraction"	"bioassay_data_transformation"
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Study Protocol Description	"4 week-old male Fischer 344 rats were purchased from Charles River Japan. They were housed in an air-conditioned room at 22±2 deg C and 55±15% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (CRF-1, Oriental Yeast Co.), with tap water ad libitum."	"Each group was composed of 4 rats. At each time point for each compound, there was a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for up to 1, 3, 7, 14, or 28 days. Control animals received corresponding volumes of vehicle."	"Total RNA was extracted from liver using RNeasy Midi Kit (Qiagen) following manufacturer's instructions."	"Amino-allyl cRNA was synthesized from 5 μg of total RNA using the SuperScript Indirect RNA Amplification System (Invitrogen). Amino-allyl cRNA was amplified by in vitro transcription reaction for 3 h, purified using the RNeasy MinElute Kit (Qiagen), and used for the fluorescent dye coupling reaction with the Cy3 or Cy5 Post-Labeling Reactive Dye Pack (GE Healthcare). Amino-allyl cRNA from individual compound-treated rats and pooled time-matched control rats were labeled with Cy3 and Cy5, respectively."	"Fragmented cRNA was obtained by heating the solution of 1× fragmentation buffer (Invitrogen), 0.75 μg of Cy3-labeled cRNA, and 0.75 μg of Cy5-labeled cRNA at 94 deg C for 15 min. 30 μl of the fragmented mixture, 46.5 μl of water, 37.5 μl of 20× SSC, 7.5 μl of 10% SDS, and 12 μl of 5× Denhardt's solution were mixed and heated at 95 deg C for 2 min. 1.5 μl of 10 mg/ml salmon sperm DNA solution and 15 μl of formamide were added and heated at 60 deg C for 3 min. 130 μl of hybridization mixture was injected into a microarray chamber and sealed. The microarray was transferred to a hybridization chamber and incubated at 60 deg C overnight with rotation at 6 rpm. After incubation, the microarray was washed for 10 min at 30 deg C in low stringency wash buffer (5× SSC and 0.1% SDS), washed twice for 2 min at 30 deg C in high-stringency wash buffer (0.5× SSC), and finally rinsed with 0.5× SSC and 0.01% Tween20. The microarray was dried by centrifugation at 360×g for 1 min."	"Scanned on an Agilent G2565AA scanner."	"Images were quantified using GenePix Pro Software (version 4.0)."	"LOWESS normalized, background subtracted data was calculated by an R package 'sma' using processed Red signal and processed Green signal."	"ID_REF = <br>VALUE = Normalized log2 ratio (Cy3/Cy5) representing test/reference."
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STUDY CONTACTS
Study Person Last Name	"Matsumoto"
Study Person First Name	"Hiroshi"
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Study Person Email	"matsumoto-hiroshi@ceri.jp"
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Study Person Address	"Chemicals Evaluation and Research Institute, Japan, 1600 Shimotakano, Sugito-machi, Kitakatsushika-gun, Saitama , Japan"
Study Person Affiliation	"Chemicals Evaluation and Research Institute, Japan"
Study Person Roles	"submitter"
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