|
Status |
Public on Apr 23, 2009 |
Title |
NR-S1, primary tumor control (Cy5) vs. lung metastasis control (Cy3), replicate 1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
NR-S1, primary tumor control, 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: None
|
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, lung metastasis, 2 weeks after 7.5 mm, clone 1
|
Organism |
Mus musculus |
Characteristics |
Strain: C3H/HeMsNrs, Gender: male, Tumor type: NR-S1 (squamous cell carcinoma), Tumor site: metastasic tumor (lung), Time: 2 weeks after the diameter of the primary tumor had reached 7.5 mm, Irradiation: None
|
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. The primary tumors were sampled at 1 week after the diameter of the tumor became 7.5mm, and metastatic tumors were sampled at 2 weeks after the diameter of the tumor became 7.5mm. The tumor cells were collected using the laser microdissection technique, and the expression profiles of the primary tumor and the metastatic tumors 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 |