|
| Status |
Public on Jul 02, 2013 |
| Title |
sample.6 0 mg/kg DB[a,h]A |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from mouse livers labeled with Cyanine-5 (red)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: part of liver
gender: male
age: 10 weeks
genotype/variation: transgenic mouse strain 40.6
date of exposure: March 2-30
dose: 0 mg/kg DB[a,h]A
time post exposure: 3 days
|
| 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 200 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 |
vendor: Stratagene, La Jolla, CA, USA
catalog #: 740100
sample type: Total RNA derived from 11 mouse cell lines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
purchased from Stratagene
|
| Label |
Cy3
|
| Label protocol |
Individual 200 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 G4852A Microarrays (containing approximately 60,000 probes) were hybridized with 300 ng Cy5-labelled liver RNA and 300 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 |
Jan 19, 2012 |
| Last update date |
Jul 02, 2013 |
| 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 |
GPL13912 |
| Series (2) |
| GSE35215 |
Lack of hepatic response of microRNA in mice following DB[a,h]A exposure (Agilent expression) |
| GSE35509 |
Lack of hepatic response of microRNA in mice following DB[a,h]A exposure |
|
