|
| Status |
Public on Oct 03, 2012 |
| Title |
High.Dose.20 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
lung of mice
|
| Organism |
Mus musculus |
| Characteristics |
sampleID: 20
tissue: Part of lung
age: 25 week
gender: Male
genotype/variation: transgenic mouse strain 40.6
exposure: 28 days, daily
time post exposure: 3 days
dosage: 75 mg/kg/day BaP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada). RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).
|
| Label |
Cy5
|
| Label protocol |
Individual 250 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
|
| |
|
| Channel 2 |
| Source name |
universal mouse reference total RNA
|
| Organism |
Mus musculus |
| Characteristics |
catalog#: 740100
vendor: Stratagene, La Jolla, CA, USA
sample type: Total RNA derived from 11 mouse cell lines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))
|
| Label |
Cy3
|
| Label protocol |
Individual 250 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
|
| |
|
| |
| Hybridization protocol |
Agilent Mouse G4846A Microarrays (containing approximately 40,000 probes) were hybridized with 250 ng Cy5-labelled liver RNA and 250 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays. Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.
|
| Scan protocol |
Arrays were scanned scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software 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 |
Feb 10, 2012 |
| Last update date |
Oct 03, 2012 |
| Contact name |
Andrew Williams |
| Organization name |
Health Canada
|
| Street address |
50 Columbine
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1A OK9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE35718 |
Pulmonary gene expression in MutaTMMouse orally gavaged with three doses of benzo(a)pyrene and vehicle control |
|
