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Sample GSM497646 Query DataSets for GSM497646
Status Public on Jan 16, 2010
Title F1FCCX-2
Sample type RNA
 
Source name female, non-treated
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue: cerebral cortex
sex: female
chemical: non-treated
Treatment protocol MDMA ((±)-3, 4-methylenedioxymethamphetamine hydrochloride, CAS # 92279-84-0, purity ≥99.9%) was obtained from the Reproductive and Development Toxicology Division of the Toxicological Research Department, The National Institute of Toxicological Research, Seoul, Korea. MDMA was dissolved in isotonic saline at doses of 20 mg/kg at volumes corresponding to 3ml/kg, and was administered orally (p.o.).
Growth protocol Male and female C57BL/6N mice (6 weeks), purchased from the Orient Co. Ltd., were kept under SPF-conditions. All mice were acclimatized in the laboratory according to the ‘Guide for the Care and Use of Laboratory Animals’ (US NIH publication No. 86-23, 1985 Ed.)
Extracted molecule total RNA
Extraction protocol Brain regions were then dissected free, frozen on dry ice, and stored in a LN2 tank until further analysis. Total RNA was isolated from the brain tissue using the TRI reagent (Molecular Research Center, Cincinnati, OH.,USA), according to the manufacturer's instructions (Life Technology, Rockville, MD, USA). Briefly, the tissues were frozen in liquid nitrogen, pulverized, homogenized in 1 ml of TRI reagent, and incubated for 5 min at room temperature; 200 µl if chloroform was added, vigorously mixed, and incubated for 3 min at room temperature. The samples were centrifuged at 14000 rpm for 20 min, aqueous phases were transferred to fresh tubes with an equal volume of isopropanol, and incubated on ice for 30 min. After centrifugation at 14000 rpm for 15 min, RNA pellets were washed in 75% ethanol and dissolved in RNase-free water. RNA qualities were assessed using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA), and concentrations were determined using a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Samples with a minimum 28S/18S ratio of > 1.6 were selected for further study.
Label Digoxigenin-UTP
Label protocol 1 microgram of total RNA was used to transcribe DIG labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0
 
Hybridization protocol Fifteen microgram of DIG labeled fragmented cRNA was used for microarray hybridization and performed according to the Applied Biosystems protocols
Scan protocol Chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems 1700 Chemiluminescent Microarray Analyzer, according to the manufacturer's instructions. Images were auto-gridded and chemiluminescent signals were quantified, corrected for background, and spatially normalized.
Description N2_F1FCCX-2
Data processing For primary data filtering, spots with a SNR (Signal to Noise Ratio) <1.5 were excluded, and the remaining filtered data were used for further analysis. Quantile normalization was used to normalize data. All process performed using GenPlex software (Istech Inc., Korea)
 
Submission date Jan 15, 2010
Last update date Oct 18, 2022
Contact name Jung Woo Eun
E-mail(s) jetaimebin@catholic.ac.kr
Organization name Ajou University of Korea
Street address Department of Gastroenterology
City Suwon, Korea
State/province Korea
ZIP/Postal code 16499
Country South Korea
 
Platform ID GPL2995
Series (1)
GSE19914 Identification of post-generation effect of MDMA on the mouse brain by large-scale gene expression analysis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
297784 15.28267
297907 10.065245
297912 13.214336
297935 11.892812
297990 9.655372
297993 9.338213
298000 14.282265
298038 10.807167
298121 10.000574
298130
298143 15.8783045
298150
298151 9.380717
298155
298165 15.451774
298174 11.75922
298188 9.85921
298200 17.79348
298246
298248

Total number of rows: 33012

Table truncated, full table size 432 Kbytes.




Supplementary file Size Download File type/resource
GSM497646.txt.gz 689.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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