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Sample GSM442747 Query DataSets for GSM442747
Status Public on Nov 24, 2009
Title BS-Wildtype-Vehicle-rep1
Sample type RNA
 
Source name brain stem, wildtype mouse, chronic treatment with vehicle
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wildtype
sex: male
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 5.77819295
ILMN_1212612 11.50394424
ILMN_1212619 7.381433249
ILMN_1212628 4.843538412
ILMN_1212632 6.493044099
ILMN_1212636 10.76819464
ILMN_1212637 8.426988649
ILMN_1212645 9.014989551
ILMN_1212648 8.754010421
ILMN_1212653 9.698123673
ILMN_1212672 7.534093875
ILMN_1212682 6.413263284
ILMN_1212683 4.989459214
ILMN_1212685 4.859923522
ILMN_1212692 6.160480587
ILMN_1212693 7.798314249
ILMN_1212695 5.920089354
ILMN_1212698 4.637826531
ILMN_1212702 13.70452935
ILMN_1212703 7.686088238

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary file Size Download File type/resource
GSM442747_4266965013_A.txt.gz 11.1 Mb (ftp)(http) TXT
GSM442747_4266965013_A_Grn.tif.gz 53.7 Mb (ftp)(http) TIFF
Raw data provided as supplementary file
Processed data included within Sample table

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