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Sample GSM442757 Query DataSets for GSM442757
Status Public on Nov 24, 2009
Title BS-Disc1Mutant-Vehicle-rep2
Sample type RNA
 
Source name brain stem, L100P mutant mouse, chronic treatment with vehicle
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: mutation Disc1 ENU L100P/L100P
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 5.037892792
ILMN_1212612 11.31933595
ILMN_1212619 6.862064449
ILMN_1212628 5.816455594
ILMN_1212632 6.596742548
ILMN_1212636 11.0777363
ILMN_1212637 8.537056582
ILMN_1212645 8.654788163
ILMN_1212648 8.452030389
ILMN_1212653 9.688596332
ILMN_1212672 7.349037317
ILMN_1212682 5.770562973
ILMN_1212683 5.059894029
ILMN_1212685 5.172676133
ILMN_1212692 6.392226998
ILMN_1212693 7.940586988
ILMN_1212695 5.594445504
ILMN_1212698 4.939089905
ILMN_1212702 13.29102962
ILMN_1212703 7.107052126

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary file Size Download File type/resource
GSM442757_4266965059_A.txt.gz 11.2 Mb (ftp)(http) TXT
GSM442757_4266965059_A_Grn.tif.gz 53.3 Mb (ftp)(http) TIFF
Raw data provided as supplementary file
Processed data included within Sample table

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