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Sample GSM831340 Query DataSets for GSM831340
Status Public on Aug 14, 2012
Title 10 mg/kg MPH tr1001
Sample type RNA
 
Source name mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse
Organism Mus musculus
Characteristics strain: Swiss Webster
treatment: 10mg/kg MPH
tissue: substantia nigra
Extracted molecule total RNA
Extraction protocol mRNA was isolated from SN in accordance with the protocol outlined in RNAqueous-Micro kit (Ambion, Austin, TX) according to manufacturer's recommendations.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix expression protocol from 100 nanograms total RNA (GeneChip 3' IVT Expression Kit, P/N 702646 Rev. 5).
 
Hybridization protocol Following fragmentation, 5 microgram of cRNA were hybridized for 16 hr at 45C on HT MG-430 PM array plate. Arrays were washed and stained in the Affymetrix GeneTitan.
Scan protocol Arrays were scanned using the Affymetrix GeneTian
Description Gene expression data from mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse
Data processing The data were normalized using RMA method with arrays on the plate. Batch correction was done using ComBat.
 
Submission date Nov 10, 2011
Last update date Aug 14, 2012
Contact name Chunxu Qu
E-mail(s) chunxu.qu@stjude.org
Phone 9015952433
Organization name St Jude Children's Research Institute
Department Pathology
Lab Mullighan
Street address 262 Danny Thomas Pl
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL11180
Series (1)
GSE33619 Methylphenidate exposure induces dopamine neuron loss and activation of microglia in the basal ganglia of mice

Data table header descriptions
ID_REF
VALUE RMA-normalized and ComBat-corrected, log2 transformed Signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 6.9979
AFFX-BioB-M_at 8.1976
AFFX-BioB-3_at 8.0819
AFFX-BioC-5_at 9.0614
AFFX-BioC-3_at 9.1970
AFFX-BioDn-5_at 10.3313
AFFX-BioDn-3_at 11.5533
AFFX-CreX-5_at 12.9045
AFFX-CreX-3_at 12.9713
AFFX-DapX-5_at 7.0842
AFFX-DapX-M_at 8.1585
AFFX-DapX-3_at 9.4965
AFFX-LysX-5_at 3.7796
AFFX-LysX-M_at 5.1688
AFFX-LysX-3_at 6.2722
AFFX-PheX-5_at 4.8386
AFFX-PheX-M_at 5.6243
AFFX-PheX-3_at 6.5515
AFFX-ThrX-5_at 4.6264
AFFX-ThrX-M_at 5.2695

Total number of rows: 45141

Table truncated, full table size 946 Kbytes.




Supplementary file Size Download File type/resource
GSM831340_tr1001_htmg430pm24.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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