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Sample GSM234672 Query DataSets for GSM234672
Status Public on Apr 23, 2009
Title NR-S1, primary tumor carbon 5 Gy (Cy5) vs. primary tumor gamma 8 Gy (Cy3), replicate 1
Sample type RNA
 
Channel 1
Source name NR-S1, primary tumor carbon ion 5 Gy, 1 week after 7.5 mm, clone 1
Organism Mus musculus
Characteristics Strain: C3H/HeMsNrs, Gender: male, Tumor type: NR-S1 (squamous cell carcinoma), Tumor site: primary tumor (hind leg), Time: 1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation: carbon ion 5 Gy on the primary tumor when the diameter is 7.5 mm
Treatment protocol Tumor cells were collected selectively by laser-microdissection technique, and the RNA was extracted from the tumor cells.
Extracted molecule total RNA
Extraction protocol RNeasy Micro Kit (QIAGEN)
Label Cy5
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification Kit
 
Channel 2
Source name NR-S1, primary tumor gamma ray 8 Gy, 1 week after 7.5 mm, clone 1
Organism Mus musculus
Characteristics Strain: C3H/HeMsNrs, Gender: male, Tumor type: NR-S1 (squamous cell carcinoma), Tumor site: primary tumor (hind leg), Time: 1 week after the diameter of the primary tumor had reached 7.5 mm, Irradiation: gamma ray 8 Gy on the primary tumor when the diameter is 7.5 mm
Treatment protocol Tumor cells were collected selectively by laser-microdissection technique, and the RNA was extracted from the tumor cells.
Extracted molecule total RNA
Extraction protocol RNeasy Micro Kit (QIAGEN)
Label Cy3
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification Kit
 
 
Hybridization protocol according to standard Agilent protocol
Scan protocol Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).
Description Murine squamous cell carcinoma, NR-S1, was transplanted into the hind leg of C3H/HeMsNrs mice. When the diameter of the primary tumors became 7.5mm, one group received 5 Gy of carbon ion irradiation, and another group received 8 Gy of gamma ray irradiation on the primary tumors. After 1 week, the primary tumors were sampled, and the tumor cells were collected using the laser microdissection technique. The expression profiles of the carbon-ion irradiated primary tumor and gamma-ray-irradiated tumor were compared using the two-color method.
Data processing Dye biases between two signals, Red and Green, were corrected using Lowess normalization, subtracted background and converted to log10 of processed Red signal/processed Green signal.
 
Submission date Oct 04, 2007
Last update date Aug 14, 2011
Contact name Kaori Imadome
Organization name National institute of radiological sciences
Department Research Center of Charged Particle Therapy
Lab RadGenomics Project
Street address Anagawa 4-9-1
City Chiba
State/province Chiba
ZIP/Postal code 2658333
Country Japan
 
Platform ID GPL4134
Series (1)
GSE9305 Gene expression profiles of primary tumors with radiotherapy and lung metastases in mouse squamous cell carcinoma model.

Data table header descriptions
ID_REF Agilent feature number
VALUE (base 10) log(REDsignal/GREENsignal) per feature (processed signals used)
LogRatioError Error of the log ratio calculated according to the error model chosen
PValueLogRatio Significance level of the Log Ratio computed for a feature
gProcessedSignal Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio
rProcessedSignal Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio

Data table
ID_REF VALUE LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal
1 5.27E-02 6.16E-02 3.92E-01 7.12E+03 8.04E+03
2 0.00E+00 6.12E-01 1.00E+00 7.01E+00 6.39E+00
3 0.00E+00 6.13E-01 1.00E+00 7.00E+00 6.38E+00
4 0.00E+00 6.12E-01 1.00E+00 6.99E+00 6.37E+00
5 0.00E+00 6.12E-01 1.00E+00 6.97E+00 6.36E+00
6 0.00E+00 6.12E-01 1.00E+00 6.96E+00 6.35E+00
7 0.00E+00 6.12E-01 1.00E+00 6.95E+00 6.33E+00
8 0.00E+00 6.12E-01 1.00E+00 6.93E+00 6.32E+00
9 0.00E+00 6.12E-01 1.00E+00 6.91E+00 6.30E+00
10 0.00E+00 6.12E-01 1.00E+00 6.89E+00 6.28E+00
11 0.00E+00 6.12E-01 1.00E+00 6.87E+00 6.27E+00
12 -1.40E-01 5.48E-01 7.99E-01 8.59E+00 6.23E+00
13 1.97E-01 4.63E-01 6.70E-01 6.88E+00 1.08E+01
14 0.00E+00 6.12E-01 1.00E+00 6.80E+00 6.21E+00
15 3.31E-01 3.24E-01 3.06E-01 8.37E+00 1.79E+01
16 2.27E-02 6.27E-02 7.17E-01 3.08E+02 3.25E+02
18 0.00E+00 6.14E-01 1.00E+00 6.71E+00 6.12E+00
19 0.00E+00 6.13E-01 1.00E+00 6.68E+00 6.10E+00
20 -1.20E-02 1.07E-01 9.11E-01 4.51E+01 4.39E+01
21 -1.89E-01 5.18E-01 7.16E-01 9.30E+00 6.03E+00

Total number of rows: 45018

Table truncated, full table size 2247 Kbytes.




Supplementary file Size Download File type/resource
GSM234672.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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