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Sample GSM1062422 Query DataSets for GSM1062422
Status Public on Sep 27, 2013
Title 50mg/kg Sample 14
Sample type RNA
 
Channel 1
Source name 50mg/kg
Organism Mus musculus
Characteristics strain: MutaTMMouse
tissue: Forestomach
gender: Male
Treatment protocol Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of BaP dissolved in olive oil were selected to dose the animals: 25 mg/kg BW, 50 mg/kg BW, and 75 mg/kg BW. Control animals were gavaged with olive oil only. Tissues were collected 72 hours following the final dose.
Growth protocol Male MutaTMMouse, aged 24-26 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. 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.
Extracted molecule total RNA
Extraction protocol Mice were anaesthetized under isofluorane followed by exsanguination. Murine forestomachs 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 (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 > 6.6.
Label Cy5
Label protocol 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.
 
Channel 2
Source name Universal Mouse Reference RNA
Organism Mus musculus
Characteristics tissue: 11 mouse cell lines
Treatment protocol Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of BaP dissolved in olive oil were selected to dose the animals: 25 mg/kg BW, 50 mg/kg BW, and 75 mg/kg BW. Control animals were gavaged with olive oil only. Tissues were collected 72 hours following the final dose.
Growth protocol Male MutaTMMouse, aged 24-26 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. 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.
Extracted molecule total RNA
Extraction protocol Mice were anaesthetized under isofluorane followed by exsanguination. Murine forestomachs 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 (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 > 6.6.
Label Cy3
Label protocol 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.
 
 
Hybridization protocol Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol. Samples were hybridized for 17 hours at 65oC and 10 rpm.
Scan protocol Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations. Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.
Data processing 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.
 
Submission date Jan 11, 2013
Last update date Sep 27, 2013
Contact name Sarah Labib
Organization name Health Canada
Street address 204b-50 Colombine
City Ottawa
State/province Ontario
ZIP/Postal code K1A0K9
Country Canada
 
Platform ID GPL10787
Series (1)
GSE43438 Sub-chronic forestomach transcriptional response in adult male MutaTMMouse following oral exposure to benzo(a)pyrene

Data table header descriptions
ID_REF
VALUE Sample represents the lowess normalized log2 ratio (sample(Cy5)/reference(Cy3))

Data table
ID_REF VALUE
A_55_P2051983 0.132416451
A_52_P169082 0.912971394
A_30_P01028193 0.116430579
A_52_P237997 -0.033153123
A_51_P414243 0.680488295
A_55_P2136348 -0.463892138
A_30_P01033363 -0.418589982
A_55_P2049737 0.229052769
A_30_P01024440 0.265382129
A_30_P01025554 1.306749928
A_30_P01031558 0.047435452
A_30_P01030675 -0.193184282
A_51_P328014 -0.347704927
A_30_P01019108 0.03018135
A_55_P2056220 0.110699165
A_55_P1985764 -0.430432685
A_52_P108321 0.216974241
A_55_P2018002 0.207045742
A_52_P123354 1.613091736
A_30_P01023685 -0.25361388

Total number of rows: 55681

Table truncated, full table size 1438 Kbytes.




Supplementary file Size Download File type/resource
GSM1062422_252800510954_201204121002_S01_GE2_1010_Sep10_2_3.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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