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Sample GSM351185 Query DataSets for GSM351185
Status Public on Sep 05, 2009
Title Hippocampus-SRRmutant-rep1
Sample type RNA
 
Source name SRR mutant hippocampus
Organism Mus musculus
Characteristics Strain: C57BL/6, Gender: male, Age: 9 weeks, Tissue: hippocampus, SRR-Genotype: mutant
Treatment protocol Animals were sacrificed by cervical dislocation and brain regions were immediately dissected while being kept cool with partially frozen ASCF (124 mM NaCl, 26 mM NaHCO3, 10 mM Glucose, 3.3 mM KCl, 1 mM NaHPO4, 2 mM CaCl2, 2 mM MgCl2). Tissue was then frozen using liquid nitrogen (Praxair).
Growth protocol All animal procedures were approved by the Animal Management Committee of Mount Sinai Hospital and complied with the requirements of the Province of Ontario Animals for Research Act 1971 and the Canadian Council on Animal Care. Groups of 3-5 littermates were housed by sex in polycarbonate cages, and given ad libitum sterile food (Purina mouse chow) and water. The vivarium was maintained under a controlled temperature (21ºC ± 1ºC), and humidity (50-60%), with a 12-h diurnal cycle (lights on: 0700-1900). Animals with the SrrY269* mutation used in experiments contained >99.6% of the C57BL/6J genome. The microarray study was conducted on experimentally naïve male mice that were 9 weeks of age.
Extracted molecule total RNA
Extraction protocol Dissected tissue from whole brain, hippocampus, frontal cortex, and cerebellum was homogenized in 1mL of Trizol (Invitrogen) using a Polytron homogenizer (PRO Scientific). A 5-min incubation at room temperature preceded and followed the addition of 200 μL of chloroform (Sigma). Samples were centrifuged at 12,000 × g for 15 min at 4°C and the aqueous phase was collected. Total RNA was precipitated from the aqueous phase using 500 μL of isopropyl alcohol (Sigma), and samples were then incubated at room temperature for 10 min and centrifuged at 12,000 × g for 10 min at 4°C. The RNA pellet was washed with 1 mL of 75% ethanol, centrifuged at 7,500 × g for 5 min at 4°C, and dissolved in 100 μL of DEPC-treated water (Applied Biosystems). For the microarray experiment, additional purification of total RNA was completed with the Absolutely RNeasy RT-PCR Miniprep kit (Strategene). RNA yield was quantified by UV spectrophotometry (NanoDrop ND-1000; Thermo Fisher Scientific) and RNA integrity was verified using the Agilent Bioanalyzer 2100 system (Agilent Technologies).
Label biotin
Label protocol Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).
 
Hybridization protocol Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX). 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 BeadScan software was used for the identification of bead positions and the extraction of raw-data.
Description Hippocampus-SRRmutant-rep1
Data processing Illumina data was pre-processed separately and identically for each tissue. All pre-processing was performed in the R statistical environment (v2.7.2) using the BioConductor open-source library (Gentleman RC et al. Genome Biol 2004). Raw array data (TIFF files) were first processed using the beadarray package (v1.8.0) (Dunning MJ et al. Bioinformatics 2007). The raw data was subsequently background-corrected using the non-linear Edwards model (Edwards D Bioinformatics 2003). Following careful quality assessment at the bead and gene level, no arrays were excluded. The background-corrected data was summarized in normal space using the standard Illumina method. The summarized data was transformed using the vst method as implemented in the lumi package (v1.6.2) (Lin SM et al. Nucleic Acids Res 2008), and then normalized using quantile splines (Workman C et al. Genome Biol 2002).
 
Submission date Dec 15, 2008
Last update date Sep 05, 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)
GSE13974 Genetic inactivation of serine racemase produces behavioral phenotypes related to schizophrenia in mice

Data table header descriptions
ID_REF
VALUE Bead-level data background-corrected using the non-linear Edwards model, summarized in normal space using the standard Illumina method, vst transformed, and quantile-spline-normalized.

Data table
ID_REF VALUE
ILMN_1250052 7.76
ILMN_3122480 7.57
ILMN_2599935 8.71
ILMN_2675543 7.53
ILMN_2686883 7.85
ILMN_2751818 8.04
ILMN_2728634 7.64
ILMN_3040515 7.54
ILMN_2711608 7.54
ILMN_1232875 7.68
ILMN_1258507 7.53
ILMN_2746142 7.54
ILMN_1253709 7.58
ILMN_1231129 11.88
ILMN_2711788 7.52
ILMN_2707099 7.72
ILMN_2942000 8.33
ILMN_2642403 13.39
ILMN_2935636 7.57
ILMN_1242024 7.93

Total number of rows: 25697

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM351185.tif.gz 53.1 Mb (ftp)(http) TIFF
GSM351185.txt.gz 11.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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