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Sample GSM153534 Query DataSets for GSM153534
Status Public on Dec 26, 2007
Title LT489 wild-type after nicotine-induced seizures
Sample type RNA
 
Source name Wild-type mice following nicotine-induced seizures
Organism Mus musculus
Characteristics Strain: C57BL/6J
Gender: F
Age: 7 weeks
Treatment: 1 hour following nicotine-induced seizures
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)
Label biotin-labeled
Label protocol 10 mg of total RNA were used to synthesize double-stranded cDNA with the Superscript Choice System (Invitrogen, Carlsbad, CA) and 100 pmole of oligo-dT primer attached to a T7 promoter sequence (Genset, Paris, France). The double-stranded cDNAs were phenol/chloroform extracted with Phase Lock Gels tubes (Eppendorf, Hamburg, Germany). In vitro transcription (IVT) of the double-stranded cDNA products was performed with an Enzo BioArray High Yield Transcript labeling kit in the presence of biotin-labeled nucleotides (Affymetrix, Inc., Santa Clara, CA). Following purification by an RNeasy mini kit (Qiagen Sciences), the biotin-labeled cRNA products were subjected to alkaline lysis (200mM Tris-acetate pH 8.1, 500mM potassium acetate, 150mM magnesium acetate).
 
Hybridization protocol Fragmented cRNAs were hybridized overnight at 45°C to Affymetrix Gene Chip Murine Genome U74Avr2 arrays (Affymetrix, Inc.).
Scan protocol Affymetrix Gene-Array Scanner
Description Total RNA was extracted from whole brain. Total RNA isolation, target preprocessing and hybridization to the U74Av2 microarray were conducted according to Affymetrix’s instructions.
Data processing The signal values were generated by statistical algorithm implanted in Affymetrix Suite Version 5.0 software (MAS5, Affymetrix, Inc.) The detection calls were calculated, based on the detection p-value, as following: probe sets with p-value of more than 0.06 were designated as absent, p-value of more than 0.04 and less than 0.06 as marginal and p-value of less than 0.04 as present. For interarray comparisons, data from each array was scaled using MAS5 software, and the mean intensity for each array was adjusted by a scaling factor to a set target intensity of 150.
 
Submission date Dec 26, 2006
Last update date Jan 05, 2007
Contact name Avi Orr-Urtreger
E-mail(s) aviorr@tasmc.health.gov.il
Phone 972-3-697-4704
Fax 972-3-697-4555
Organization name Tel Aviv Sourasky Medical Center
Department Genetic Institute
Lab Research and Development Laboratory
Street address 6 Weizmann St
City Tel Aviv
ZIP/Postal code 64239
Country Israel
 
Platform ID GPL81
Series (1)
GSE6614 Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks

Data table header descriptions
ID_REF
VALUE signal value designates a relative measure of the abundance of the transcript
ABS_CALL indicates the reliability of the transcript’s detection call
DETECTION-P-VALUE present (P), absent (A) or marginal (M). calculated based on the detection p-value

Data table
ID_REF VALUE ABS_CALL DETECTION-P-VALUE
AFFX-MurIL2_at 6.44862 A 0.834139
AFFX-MurIL10_at 3.11566 A 0.699394
AFFX-MurIL4_at 1.694 A 0.904333
AFFX-MurFAS_at 3.71949 A 0.645547
AFFX-BioB-5_at 111.707 P 0.00255552
AFFX-BioB-M_at 326.396 P 6.02111e-05
AFFX-BioB-3_at 164.221 P 0.000389797
AFFX-BioC-5_at 567.92 P 0.000146581
AFFX-BioC-3_at 351.752 P 4.42873e-05
AFFX-BioDn-5_at 455.301 P 4.42873e-05
AFFX-BioDn-3_at 2350.98 P 9.4506e-05
AFFX-CreX-5_at 4123.55 P 4.42873e-05
AFFX-CreX-3_at 6690.6 P 4.42873e-05
AFFX-BioB-5_st 15.5802 A 0.39692
AFFX-BioB-M_st 27.6202 A 0.470241
AFFX-BioB-3_st 9.3611 A 0.760937
AFFX-BioC-5_st 6.28969 A 0.891021
AFFX-BioC-3_st 3.71333 A 0.749204
AFFX-BioDn-5_st 67.0781 A 0.108979
AFFX-BioDn-3_st 72.3098 P 0.0166701

Total number of rows: 12488

Table truncated, full table size 364 Kbytes.




Supplementary file Size Download File type/resource
GSM153534.CEL.gz 2.7 Mb (ftp)(http) CEL
GSM153534.CHP.gz 4.6 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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