NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM671520 Query DataSets for GSM671520
Status Public on Feb 13, 2011
Title Animal 169 (-Seizures) Left technical rep 2
Sample type RNA
 
Source name Animal 169 (-Seizures) Left
Organism Rattus norvegicus
Characteristics tissue: Dentate gyrus
seizure: -
side: left
Treatment protocol Adult male rats were given atropine (0.04 mg i.m.), anesthetized with isofluorane 2%, and unilaterally injected with kainic acid (KA; 0.2 µl; 2.0 µg/µl normal saline) in the right posterior CA3 area of hippocampus (AP= -5.6 mm, ML= 4.0 mm, DV= 7.0 mm. A 30ga. needle attached to a Hamilton 1.0 µl syringe was lowered into the injection site and after 5 minutes, one half of the volume was injected. After another 5 minutes, the needle was raised 0.5 mm and the remainder of the solution was injected. After 20 minutes, the needle was withdrawn.
Growth protocol Beginning 2 months after kainate injection, video monitoring was performed for all rats in order to detect spontaneous behavioral seizures. After eight months of video monitoring rats were divided for electrophysiological (n=12), microarray (n=10).
Extracted molecule total RNA
Extraction protocol Ten rats were taken for microarray studies: five with documented behavioral spontaneous seizures and five rats without spontaneous seizures. Rats were anesthetized with isofluorane, brains were quickly removed and sectioned by vibratome into 400 µm slices. Dentate gyri were removed under dissecting microscope and placed in -80C for further microarray experiments. The comparisons were performed between the area of dentate gyri (DG) adjacent to the KA lesion and non-lesioned contralateral side in each animal. RNA extraction was performed using Trizol (Invitrogen). RNA concentration and quality were evaluated using Nanodrop ND-1000 spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyser (Agilent).
Label cy5
Label protocol We used 100 ng of RNA as the initial starting template, which was labeled with biotin using the low input fluorescent linear amplification kit (Agilent). The labeled cRNA concentration was verified (Nanodrop) and RNA quality was checked on an Agilent Bioanalyzer (Agilent).
 
Hybridization protocol The microarray hybridizations were performed according to manufacturer's protocols.
Scan protocol The microarray scanning were performed according to manufacturer's protocols.
Description L dg -Seizures
Data processing We imported the raw data from the Codelink microarrays into R (http://www.r-project.org/). We used available libraries from Bioconductor (http://www.bioconductor.org/) to analyze the one-color microarray design. We used the linear models package (LIMMA). After the removal of flagged data, we used the default method for background subtraction and used quantile normalization to normalize values between arrays.
 
Submission date Feb 08, 2011
Last update date Feb 13, 2011
Contact name Kellen Winden
Organization name Boston Children's Hospital
Department Neurology
Street address 300 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL2896
Series (2)
GSE27166 Rat model of MTLE: Animals with epilepsy vs animals without epilepsy (codelink)
GSE27268 Rat model of MTLE: Animals with epilepsy vs animals without epilepsy

Data table header descriptions
ID_REF
VALUE quantile normalized with controls removed

Data table
ID_REF VALUE
1002 0.447662239
1004 0.453579155
1005 55.12996559
1006 4.670946019
1009 1.981569015
1010 0.035044022
1011 0.541077038
1012 6.55742568
1013 26.18319488
1016 0.194945083
1017 0.096967816
1018 0.698588195
1019 0.047423759
1020 27.53729895
1023 4.070150887
1024 1.773918841
1025 0.513025483
1026 3.783654238
1027 3.062505589
1030 0.046225088

Total number of rows: 33441

Table truncated, full table size 603 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap