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Sample GSM239971 Query DataSets for GSM239971
Status Public on Jan 01, 2008
Title St6gal1-/- tumor #3376
Sample type RNA
 
Source name PyV-mT St6gal1-/- 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 5247.54 P 0.000445901
AFFX-BioB-M_at 7796.17 P 4.42873e-05
AFFX-BioB-3_at 4263.47 P 5.16732e-05
AFFX-BioC-5_at 13294.7 P 4.42873e-05
AFFX-BioC-3_at 17532.5 P 4.42873e-05
AFFX-BioDn-5_at 22456.6 P 4.42873e-05
AFFX-BioDn-3_at 54656.2 P 4.42873e-05
AFFX-CreX-5_at 149604 P 5.16732e-05
AFFX-CreX-3_at 184228 P 4.42873e-05
AFFX-DapX-5_at 16.6952 A 0.921998
AFFX-DapX-M_at 93.9332 A 0.41138
AFFX-DapX-3_at 158.531 A 0.659339
AFFX-LysX-5_at 58.4988 A 0.514903
AFFX-LysX-M_at 27.4345 A 0.953518
AFFX-LysX-3_at 166.156 A 0.48511
AFFX-PheX-5_at 11.5674 A 0.921998
AFFX-PheX-M_at 22.2557 A 0.932322
AFFX-PheX-3_at 212.86 A 0.544587
AFFX-ThrX-5_at 55.7149 A 0.544587
AFFX-ThrX-M_at 68.3393 A 0.60308

Total number of rows: 45101

Table truncated, full table size 1378 Kbytes.




Supplementary file Size Download File type/resource
GSM239971.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM239971.CHP.gz 241.2 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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