Comment[ArrayExpressAccession]	E-GEOD-43633
MAGE-TAB Version	1.1													
Public Release Date	2015-07-01
Investigation Title	Acute hepatic transcriptional response in male mice following oral exposure to benzo(a)pyrene													
Comment[Submitted Name]	Acute hepatic transcriptional response in male mice following oral exposure to benzo(a)pyrene
Experiment Description	Benzo(a)pyrene is a well-established human carcinogen in humans and rodents. In the present study, we sought to determine the dose- and time-dependent changes in gene expression upon oral exposure to benzo(a)pyrene. Adult male B6C3F1 mice were exposed to four doses of benzo(a)pyrene or vehicle control for three days and sacrificed 4 or 24 hours after the final exposure. This experiment examined the hepatic transcriptional response of male mice exposed to BaP for 3 days at four different doses, including D1 (300 mg/kg BW/day), D2 (150 mg/kg BW/day), D3 (50 mg/kg BW/day) and D4 (5 mg/kg BW/day), and one control.  Each dose group was further examined at 2 time points,  4 hours and 24 hours, following the final exposure.  Each dose group and time point had 4-5 biological replicates. There were a total 46 samples (arrays) included in the final analysis using a two-colour reference design.													
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl												
Person Last Name	Labib	Labib	Buick	Jackson	Williams	Moffat	Chepelev	Bourdon	Kuo	Lemieux	Malik	Halappanavar	Luijten	Yauk
Person First Name	Sarah	Sarah	Julie	Kelly	Andrew	Ivy	Nikolai	Julie	Byron	France	Amal	Sabina	Mirjam	Carole
Person Mid Initials			K			D	L	A			I			L
Person Email	geo@ncbi.nlm.nih.gov													
Person Affiliation	Health Canada													
Person Address	Health Canada, 204b-50 Colombine, Ottawa, Ontario, Canada													
Person Roles	submitter													
Protocol Name	P-GSE43633-1	P-GSE43633-5	P-GSE43633-6	P-GSE43633-2	P-GSE43633-3	P-GSE43633-4	P-GSE43633-7							
Protocol Description	The log2 of the ratio (sample (Cy5)/reference (Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R. ID_REF =  VALUE = lowess-normalized, log2 (sample (Cy5)/reference (Cy3)) ratio	Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions. Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.	Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (825ng) were co-hybridized to Agilent G4122F Whole Mouse Genome (4×44K) oligonucleotide microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Version 5.7, March 2008). Samples were hybridized for 17 hours at 65oC and 10 rpm.	Mice were dosed via oral gavage (10 ml/kg body weight) daily for three consecutive days. Four different doses of BaP dissolved in corn oil were selected to dose the animals: 5mg/kg BW, 50 mg/kg BW, 150 mg/kg BW and 300 mg/kg BW. Control animals were gavaged with corn oil only. Tissues were collected 4 hours and 24 hours following the final dose.	Male B6C3F1 mice, aged 27-30 days old, were obtained from Charles River Laboratories (St-Constant, Quebec, Canada). Animals were acclimatised for 7 days prior to commencement of the dosing regime. Animals were housed in individual cages and fed Purina rodent chow and water ad libitum, under a 12h light/12h dark lighting schedule. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.	Mice were anaesthetized under isofluorane followed by exsanguination. Murine livers were removed, placed in cryovials and immediately snap frozen in liquid nitrogen. Tissues were stored at -80oC until RNA extraction was performed. Total RNA was extracted from random sections of the right medial lobe of the liver (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 8.0.	Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505C) using the AgilentHD_GX_2Color scanning profile. Data was extracted from the scanned images using Feature Extraction Version 10.1.1.1.							
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol							
Experimental Factor Name	time	dose												
Experimental Factor Type	time	dose												
Comment[SecondaryAccession]	GSE43633													
Comment[GEOReleaseDate]	2015-07-01													
Comment[ArrayExpressSubmissionDate]	2013-01-18													
Comment[GEOLastUpdateDate]	2015-07-01													
Comment[AEExperimentType]	transcription profiling by array													
Comment[AdditionalFile:Data1]	GSE43633_Design_Data_Matrix.txt													
SDRF File	E-GEOD-43633.sdrf.txt