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Sample GSM442749 Query DataSets for GSM442749
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

Data table header descriptions
ID_REF
VALUE vsn-normalized values

Data table
ID_REF VALUE
ILMN_1212607 5.78194876
ILMN_1212612 10.98101018
ILMN_1212619 6.846057536
ILMN_1212628 5.282377685
ILMN_1212632 7.098602195
ILMN_1212636 10.9681413
ILMN_1212637 8.097529628
ILMN_1212645 9.572112326
ILMN_1212648 8.447190462
ILMN_1212653 9.80389109
ILMN_1212672 7.643854186
ILMN_1212682 5.810023898
ILMN_1212683 5.073922764
ILMN_1212685 5.227062622
ILMN_1212692 6.23382759
ILMN_1212693 7.929849694
ILMN_1212695 5.468853193
ILMN_1212698 4.935219221
ILMN_1212702 14.53909698
ILMN_1212703 7.026442469

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary file Size Download File type/resource
GSM442749_4266965022_D.txt.gz 11.4 Mb (ftp)(http) TXT
GSM442749_4266965022_D_Grn.tif.gz 53.2 Mb (ftp)(http) TIFF
Raw data provided as supplementary file
Processed data included within Sample table

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