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Sample GSM245410 Query DataSets for GSM245410
Status Public on Nov 28, 2007
Title Radiosensitive tumor-5 hours post-IR-rep1
Sample type RNA
 
Source name tumor xenografts in nude mice
Organism Homo sapiens
Characteristics Squamous cell carcinoma
Treatment protocol Tumors were excised, frozen in liquid nitrogen and stored at -80C
Growth protocol SCC-61 and nu61 xenografts were generated and allowed to grow to a volume of 150-200 mm3. At that time,tumors were either irradiated at 3Gy or left un-treated and 5 or 24 hours later they were collected for RNA purification
Extracted molecule total RNA
Extraction protocol 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 protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized on U133A Human GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Agilent GeneArray Scanner
Description Gene expression data from radiosensitive tumor, 5 hours after irradiation at 3Gy
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. The trimmed mean target intensity of each array was arbitrarily set to 700-800.
 
Submission date Nov 28, 2007
Last update date Aug 14, 2011
Contact name Nikolai N. Khodarev
E-mail(s) [email protected]
Phone 773-834-3282
Fax 773-702-1968
Organization name The University of Chicago
Department Radiation and Cellular Oncology
Street address 5841 South Maryland Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL96
Series (2)
GSE9713 Detection of genes differentially expressed in radioresistant and radiosensitive tumors before and after irradiation
GSE9716 Radioresistant and radiosensitive tumors and cell lines

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1468.1 P 0.002023
AFFX-BioB-M_at 2093.4 P 0.000169
AFFX-BioB-3_at 1060.2 P 0.002275
AFFX-BioC-5_at 4176.8 P 0.000127
AFFX-BioC-3_at 2785.6 P 0.000509
AFFX-BioDn-5_at 3908.4 P 0.000044
AFFX-BioDn-3_at 19667.3 P 0.000095
AFFX-CreX-5_at 38090.2 P 0.000044
AFFX-CreX-3_at 44716.6 P 0.000044
AFFX-DapX-5_at 35.3 A 0.5
AFFX-DapX-M_at 60.1 A 0.52976
AFFX-DapX-3_at 11.3 A 0.916408
AFFX-LysX-5_at 3.7 A 0.868639
AFFX-LysX-M_at 50.2 A 0.712257
AFFX-LysX-3_at 59.7 A 0.205732
AFFX-PheX-5_at 64 A 0.559354
AFFX-PheX-M_at 9.2 A 0.973889
AFFX-PheX-3_at 33.5 A 0.724854
AFFX-ThrX-5_at 22.2 A 0.724854
AFFX-ThrX-M_at 15.9 A 0.916408

Total number of rows: 22283

Table truncated, full table size 594 Kbytes.




Supplementary file Size Download File type/resource
GSM245410.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM245410.EXP.gz 462 b (ftp)(http) EXP
Processed data included within Sample table

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