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Sample GSM596543 Query DataSets for GSM596543
Status Public on Sep 22, 2010
Title 153599 DFI<100
Sample type RNA
 
Source name Canine primary tumor from poor responder cohort
Organism Canis lupus familiaris
Characteristics tissue: snap frozen primary tumor
genotype(breed): Mix
age (years): 9
Growth protocol Primary tumor collected at time of limb amputation
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA followed by Qiagen Rneasy cleanup was performed according to the manufacturer's instructions.
Label biotin
Label protocol One-Cycle Target Labeling and Control Reagents package (Affymetrix, Santa Clara, CA, USA) was used to synthesize cDNA from total RNA spiked with prokaryotic Poly-A RNA as a control. The Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA) was used to purify the cDNA which was then used for synthesis of biotin-labeled cRNA.
 
Hybridization protocol cRNA was purified, quantified and fragmented before hybridization with the GeneChips. Hybridized chips were washed, stained using streptavidin-conjugated phycoerythrin dye (Invitrogen, Carlsbad, CA, USA) and enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA, USA) using an Affymetrix GeneChip Fluidics Station 450.
Scan protocol The Affymetrix GeneChip scanner 3000 was used to acquire images.
Description Gene expression data from primary tumor
Data processing The data were analyzed with Expression Console (PLIER).
 
Submission date Sep 21, 2010
Last update date Sep 21, 2010
Contact name Liza Emily O'Donoghue
E-mail(s) lpfaff@rams.colostate.edu
Phone 7739836434
Organization name Colorado State University
Department Clinical Sciences
Lab Duval
Street address 300 W. Drake Rd
City Fort Collins
State/province CO
ZIP/Postal code 80523
Country USA
 
Platform ID GPL3738
Series (1)
GSE24251 Expression data from canine osteosarcoma primary tumors (Affymetrix Canine 2.0 array)

Data table header descriptions
ID_REF
VALUE PLIER data

Data table
ID_REF VALUE
AFFX-BioB-5_at 248.303
AFFX-BioB-M_at 284.115
AFFX-BioB-3_at 206.045
AFFX-BioC-5_at 579.005
AFFX-BioC-3_at 683.466
AFFX-BioDn-5_at 1347.2
AFFX-BioDn-3_at 1820.58
AFFX-CreX-5_at 6208.32
AFFX-CreX-3_at 6976.53
AFFX-DapX-5_at 543.844
AFFX-DapX-M_at 1116.23
AFFX-DapX-3_at 1354.36
AFFX-LysX-5_at 63.9025
AFFX-LysX-M_at 86.6189
AFFX-LysX-3_at 194.318
AFFX-PheX-5_at 92.3824
AFFX-PheX-M_at 133.205
AFFX-PheX-3_at 142.226
AFFX-ThrX-5_at 58.592
AFFX-ThrX-M_at 90.4992

Total number of rows: 43035

Table truncated, full table size 1190 Kbytes.




Supplementary file Size Download File type/resource
GSM596543.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM596543.CHP.gz 350.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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