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Sample GSM239972 Query DataSets for GSM239972
Status Public on Jan 01, 2008
Title wild-type tumor #3375
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
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
Reanalyzed by GSE119085

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

Data table
AFFX-BioB-5_at 4902.19 P 0.000972149
AFFX-BioB-M_at 6063.71 P 4.42873e-05
AFFX-BioB-3_at 3866.81 P 5.16732e-05
AFFX-BioC-5_at 11904.8 P 5.16732e-05
AFFX-BioC-3_at 16092.9 P 4.42873e-05
AFFX-BioDn-5_at 19262 P 4.42873e-05
AFFX-BioDn-3_at 47346.1 P 4.42873e-05
AFFX-CreX-5_at 141968 P 5.16732e-05
AFFX-CreX-3_at 163161 P 4.42873e-05
AFFX-DapX-5_at 22.8989 A 0.529762
AFFX-DapX-M_at 241.245 A 0.185131
AFFX-DapX-3_at 228.543 A 0.645547
AFFX-LysX-5_at 19.9546 A 0.672921
AFFX-LysX-M_at 26.6087 A 0.937071
AFFX-LysX-3_at 138.656 A 0.216524
AFFX-PheX-5_at 16.4726 A 0.945787
AFFX-PheX-M_at 12.8933 A 0.932322
AFFX-PheX-3_at 120.173 A 0.617401
AFFX-ThrX-5_at 46.1352 A 0.783476
AFFX-ThrX-M_at 92.4875 A 0.58862

Total number of rows: 45101

Table truncated, full table size 1379 Kbytes.

Supplementary file Size Download File type/resource
GSM239972.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM239972.CHP.gz 241.0 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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