|
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 |