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Sample GSM541460 Query DataSets for GSM541460
Status Public on Jul 19, 2010
Title hmp223 cell line [mouse mRNA]
Sample type RNA
 
Source name mouse tumor model
Organism Mus musculus
Characteristics disease state: mouse ependymoma model
tissue: Spinal
genotype: Arf null
age: embryonic
Treatment protocol tumor exicision or cell line suspension extraction
Growth protocol mouse tumors and cell lines
Extracted molecule total RNA
Extraction protocol standard Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description Gene expression data from mouse model tumor models
Data processing The data were analyzed with GCOS v1.4 software (Affymetrix, Santa Clara, CA). Signals were normalized for each array by scaling to a 2% trimmed mean of 500.
 
Submission date May 05, 2010
Last update date Oct 08, 2010
Contact name Richard James Gilbertson
E-mail(s) richard.gilbertson@stjude.org
Organization name St Jude Children's Research Hospital
Department Developmental Neurobiology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL1261
Series (1)
GSE21687 Comparative genomics matches mutations and cells to generate faithful ependymoma models

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 467.9
AFFX-BioB-M_at 750.7
AFFX-BioB-3_at 488.4
AFFX-BioC-5_at 1231.5
AFFX-BioC-3_at 1542.6
AFFX-BioDn-5_at 2867.2
AFFX-BioDn-3_at 4555.1
AFFX-CreX-5_at 11005.5
AFFX-CreX-3_at 12679.5
AFFX-DapX-5_at 111.1
AFFX-DapX-M_at 1242.4
AFFX-DapX-3_at 2704.3
AFFX-LysX-5_at 36
AFFX-LysX-M_at 255.7
AFFX-LysX-3_at 703.1
AFFX-PheX-5_at 69.7
AFFX-PheX-M_at 188.9
AFFX-PheX-3_at 401.9
AFFX-ThrX-5_at 38.8
AFFX-ThrX-M_at 171.3

Total number of rows: 45101

Table truncated, full table size 732 Kbytes.




Supplementary file Size Download File type/resource
GSM541460.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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