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Sample GSM1242558 Query DataSets for GSM1242558
Status Public on Oct 01, 2015
Title D3 Mouse 20_lung [BaA]
Sample type RNA
 
Channel 1
Source name D3_lung
Organism Mus musculus
Characteristics strain: MutaTMMouse
gender: male
age: 10 weeks
exposed to: D3; 80 mg/kg-bw/day benz(a)anthracene for 28 days
tissue: lung
tissue collection tiime: 72 hrs following the final dose
Treatment protocol Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benz(a)anthracene dissolved in olive oil were selected to dose the animals: 20 mg/kw-bw/day, 40 mg/kg-bw/day, and 80 mg/kg-bw/day. Control animals were gavaged with olive oil only. Tissues were collected 72 hours following the final dose.
Growth protocol Male MutaTMMouse, aged ~10 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 lung, liver, and 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 > 7.0.
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 sample source: 11 mouse cell lines
vendor: Stratagene, La Jolla, CA, USA
catalog #: 740100
Treatment protocol Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benz(a)anthracene dissolved in olive oil were selected to dose the animals: 20 mg/kw-bw/day, 40 mg/kg-bw/day, and 80 mg/kg-bw/day. Control animals were gavaged with olive oil only. Tissues were collected 72 hours following the final dose.
Growth protocol Male MutaTMMouse, aged ~10 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 lung, liver, and 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 > 7.0.
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.
Description Sample 17
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 Sep 30, 2013
Last update date Oct 01, 2015
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 (2)
GSE51314 Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to benz(a)anthracene in lung, liver, and forestomach tissues
GSE51321 Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to 7 individual PAHs in the lung, liver, and forestomach tissues

Data table header descriptions
ID_REF
VALUE lowess normalized log2 ratio of Cy5/Cy3

Data table
ID_REF VALUE
A_55_P2051983 0.0390457
A_52_P169082 -0.7736342
A_30_P01028193 0.1310409
A_52_P237997 -0.1539319
A_51_P414243 -0.1173164
A_55_P2136348 -0.7493116
A_30_P01033363 -0.2287943
A_55_P2049737 0.05478713
A_30_P01024440 -0.2679102
A_30_P01025554 0.08008119
A_30_P01031558 0.3906656
A_30_P01030675 0.3236107
A_51_P328014 -1.089195
A_30_P01019108 -0.6817389
A_55_P2056220 0.4421785
A_55_P1985764 -1.52167
A_52_P108321 0.1411768
A_55_P2018002 -1.051068
A_52_P123354 0.04188161
A_30_P01023685 0.08553052

Total number of rows: 55681

Table truncated, full table size 1337 Kbytes.




Supplementary file Size Download File type/resource
GSM1242558_US22502706_252800510714_S01_GE2_1010_Sep10_1_4.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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