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Sample GSM1062413 Query DataSets for GSM1062413
Status Public on Sep 27, 2013
Title Control Sample 2
Sample type RNA
 
Channel 1
Source name vehicle control
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 0.126665294
A_52_P169082 0.890963289
A_30_P01028193 -0.241391346
A_52_P237997 -0.05540528
A_51_P414243 0.093237233
A_55_P2136348 -0.476280535
A_30_P01033363 0.018116979
A_55_P2049737 0.014827715
A_30_P01024440 0.044393471
A_30_P01025554 0.794289544
A_30_P01031558 0.145328559
A_30_P01030675 -0.292651214
A_51_P328014 -0.769073248
A_30_P01019108 0.084079699
A_55_P2056220 -0.42014704
A_55_P1985764 -0.773802491
A_52_P108321 -0.061086832
A_55_P2018002 1.613843035
A_52_P123354 1.058736894
A_30_P01023685 -0.309803564

Total number of rows: 55681

Table truncated, full table size 1438 Kbytes.




Supplementary file Size Download File type/resource
GSM1062413_252800510953_201204051003_S01_GE2_1010_Sep10_2_1.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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