|
| Status |
Public on Nov 24, 2009 |
| Title |
BS-Wildtype-Vehicle-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
brain stem, wildtype mouse, chronic treatment with vehicle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wildtype
sex: female
tissue: brain stem
drug: Saline
age: 10-12 weeks
|
| Treatment protocol |
Valproate (200 mg/kg, i.p) were given chronically (twice a day 9-10 am and 5-6 pm; for 15 days). Mice were tested in PPI on the next day after the last injection. Separated cohort of mice, treated in the same manner, have been used for molegular-genetic analysis. Brains were removed on the next day after the last injection of valproate.
|
| Growth protocol |
Animals were bred and housed at the SLRI/MSH animal facility. Standard protocols were followed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard laboratory procedures for the handling of RNA were followed. All equipment was decontaminated of RNase with RNase Erase® solution followed by 90% ethanol and DEPC-treated water. Tissue was homogenized and lysed using Trizol® Reagent (Invitrogen Life Technologies Corporation, Carlsbad, CA). Chloroform was used to separate the aqueous and organic phases. The aqueous phase was washed with 70% ethanol at 0°C. Total RNA was purified from this solution using the Absolutely RNA Miniprep® kit (Stratagene, La Jolla, CA) according to the manufacturer’s instructions. Yield and quality of total RNA obtained was estimated by optical density measurements. An A260/280 value between 1.7 and 2.1 was considered relatively free of protein and suitable for further analysis. RNA samples were concentrated to approximately 0.08-0.1 µg/µL using Microcron YM-10 centrifugal filter devices (Millipore Corporation, Bedford, MA). Aliquots of 10 µL were taken and sent for microarray analysis.
|
| Label |
biotin
|
| Label protocol |
Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).
|
| |
|
| Hybridization protocol |
Labeled cRNA samples (750 ng) were then hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina, Inc., San Diego, CA) in accordance with Illumina’s standard protocols for hybridization, staining, and data acquisition.
|
| Scan protocol |
BeadChips were imaged using the Illumina BeadArray Reader (Infinium I FastScan scanner protocol), a two-channel 0.8 μm resolution confocal laser scanner. The Illumina BeadScan software (version 3, 2006) was used for the identification of bead positions and the extraction of raw-data.
|
| Description |
NA
|
| Data processing |
Raw data (TIFF files) were loaded into the beadarray package (v1.10.0) of the BioConductor open-source library in the R statistical environment (v2.8.1). Following BASH analysis using default settings to mask spatial artefacts data was pre-processed using the Edwards background correction method and normalized using variance-stabilizing normalization as implemented in the vsn package (v3.8.0).
|
| |
|
| Submission date |
Aug 20, 2009 |
| Last update date |
Aug 20, 2009 |
| Contact name |
Paul C Boutros |
| E-mail(s) |
Paul.Boutros@utoronto.ca
|
| Organization name |
Ontario Institute for Cancer Research
|
| Street address |
101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE17735 |
Analysis of altered gene expressions in valproate-treated Disc1-L100P mutant mice |
|
