|
Status |
Public on Oct 01, 2015 |
Title |
D0 Mouse 1_lung [IP] |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
D0_lung
|
Organism |
Mus musculus |
Characteristics |
strain: MutaTMMouse gender: male age: ~13 weeks exposed to: D0; vehicle control 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 indeno(123,cd)pyrene dissolved in olive oil were selected to dose the animals: 12.5 mg/kw-bw/day, 25 mg/kg-bw/day, and 50 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 ~13 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 (D0 n=4, D1 n=5, D2 n=5, D3 n=5) 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 > 7.1.
|
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 indeno(123,cd)pyrene dissolved in olive oil were selected to dose the animals: 12.5 mg/kw-bw/day, 25 mg/kg-bw/day, and 50 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 ~13 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 (D0 n=4, D1 n=5, D2 n=5, D3 n=5) 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 > 7.1.
|
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 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 |
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) |
GSE51320 |
Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to indeno(123,cd)pyrene in lung, liver, and forestomach tissues [IP] |
GSE51321 |
Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to 7 individual PAHs in the lung, liver, and forestomach tissues |
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