|
| Status |
Public on Oct 18, 2010 |
| Title |
AF_251332613307 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Veh 1.5 h
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
sex: Male
age: 6-8 weeks
strain: CD-1
treatment: Vehicle Control
time: 1.5 h
hybridization group: Hybridization Block 1
|
| Treatment protocol |
Mice were divided into four groups of 10 and given one of following treatments: 1) vehicle control (25mM Hepes, pH 6.0, 500 mM NaCl, 6% glycerol, 0.5% Ethanol, 0.05% MSA; 2) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) dissolved in vehicle; 3) Interferon β (3.75 x 107 U/kg) dissolved in vehicle; 4) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) + Interferon β (PBL Biomedical Laboratories USA NJ )(3.75 x 107 U/kg) dissolved in vehicle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON Canada) and purified using Rneasy Mini Kits (QIAgen Inc., Mississauga, ON, Canada). RNA quantity was measured using a Spectrophotometer (ND-1000 Nanodrop technologies) and RNA quality was measured using an Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip (Agilent Technologies, Canada Inc., Mississauga, ON, Canada.)
|
| Label |
Cy5
|
| Label protocol |
Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)
|
| Organism |
Mus musculus |
| Characteristics |
reference: Total RNA derived from 11 mouse cell lines
hybridization group: Hybridization Block 1
|
| Biomaterial provider |
Stratagene, La Jolla, CA, USA
|
| Treatment protocol |
Mice were divided into four groups of 10 and given one of following treatments: 1) vehicle control (25mM Hepes, pH 6.0, 500 mM NaCl, 6% glycerol, 0.5% Ethanol, 0.05% MSA; 2) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) dissolved in vehicle; 3) Interferon β (3.75 x 107 U/kg) dissolved in vehicle; 4) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) + Interferon β (PBL Biomedical Laboratories USA NJ )(3.75 x 107 U/kg) dissolved in vehicle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
purchased from Stratagene
|
| Label |
Cy3
|
| Label protocol |
Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).
|
| |
|
| |
| Hybridization protocol |
Agilent Mouse G4121B Microarrays (containing approximately 22,000 probes) were hybridized with 5 µg Cy5-labelled liver RNA and 5 µg Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays. Arrays were incubated overnight at 60 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.
|
| Scan protocol |
Arrays were scanned using a ScanArray Express (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, CA, USA).
|
| Description |
AF_251332613307_S01_GE2-v4_95_Feb07.txt
|
| Data processing |
The median signal intensity of each microarray sample were lowess normalized. Technical replicates were not averaged. Data for each probe was flagged (flag=1) if the median signal intensity for that probe was less than the mean of the negative controls ((-)3xSLv1) plus three standard deviations.
|
| |
|
| Submission date |
Nov 09, 2009 |
| Last update date |
Oct 18, 2010 |
| 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 |
GPL2881 |
| Series (1) |
| GSE18949 |
Modulation of the transcriptional response to recombinant IFN-β by Acetaminophen |
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