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Sample GSM239970 Query DataSets for GSM239970
Status Public on Jan 01, 2008
Title wild-type tumor #3152
Sample type RNA
 
Source name PyV-mT wild-type tumor
Organism Mus musculus
Characteristics Strain: C57BL/6
Gender: female
Age: 110 days
Tissue: mammary tumor
Days after tumor onset: 14 days
Extracted molecule total RNA
Extraction protocol The tumor tissue (100 mg) was homogenized in Ultraspec (Biotecx Labs, Houston, TX), and total RNA was extracted according to the manufacturer's protocol.
Label Biotin (Affymetrix IVT)
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized on Murine Genome 430 2.0 Array GeneChip. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Six PyV-mT St6gal1 null and wild-type tumor pairs were used, in four independent pools of three tumors each.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date Oct 27, 2007
Last update date Aug 28, 2018
Contact name Maria Hedlund
E-mail(s) mahedlund@ucsd.edu
Organization name UCSD
Street address 9500 Gilman Dr CMM-E #1087
City La Jolla
State/province CA
ZIP/Postal code 92093-0687
Country USA
 
Platform ID GPL1261
Series (1)
GSE9447 Alpha2-6-linked Sialic Acids on N-Glycans Modulate Carcinoma Differentiation In Vivo
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE MAS 5.0 signal
ABS_CALL MAS 5.0 detection call
DETECTION P-VALUE MAS 5.0 detection p-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 5003.25 P 0.00010954
AFFX-BioB-M_at 6521.95 P 4.42873e-05
AFFX-BioB-3_at 3728.22 P 4.42873e-05
AFFX-BioC-5_at 13873.5 P 5.16732e-05
AFFX-BioC-3_at 18749.9 P 4.42873e-05
AFFX-BioDn-5_at 30535.8 P 4.42873e-05
AFFX-BioDn-3_at 54141.7 P 4.42873e-05
AFFX-CreX-5_at 156566 P 5.16732e-05
AFFX-CreX-3_at 183767 P 4.42873e-05
AFFX-DapX-5_at 18.3793 A 0.749204
AFFX-DapX-M_at 183.42 A 0.340661
AFFX-DapX-3_at 38.0312 A 0.904333
AFFX-LysX-5_at 8.35902 A 0.824672
AFFX-LysX-M_at 32.6607 A 0.868639
AFFX-LysX-3_at 25.4824 A 0.470241
AFFX-PheX-5_at 17.6686 A 0.84329
AFFX-PheX-M_at 17.0078 A 0.897835
AFFX-PheX-3_at 263.294 A 0.354453
AFFX-ThrX-5_at 44.9285 A 0.794268
AFFX-ThrX-M_at 185.347 A 0.205732

Total number of rows: 45101

Table truncated, full table size 1382 Kbytes.




Supplementary file Size Download File type/resource
GSM239970.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM239970.CHP.gz 240.0 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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