|
| Status |
Public on Sep 27, 2010 |
| Title |
Bone marrow_irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_irradiated_Zn-yeast_6hr (Cy3) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
bone marrow, X-ray irradiation, methylcellulose administration, 6 hours
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeSlc
gender: male
age: 10 weeks
tissue: bone marrow
irradiation: whole body irradiation
treatment: methylcellulose
|
| Treatment protocol |
0.3 ml of a 0.5% methylcellulose solution was administered i.p. to C3H mice immediately after 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after irradiation, the bone marrow was flushed from femora and was collected into centrifuge tubes.
|
| Growth protocol |
The mice, received at 8 weeks of age, were housed five per cage and allowed free access to a commercial diet (MB-1, Funabashi Farm Co., Funabashi, Japan) and acidified water during the experimental period. The animal rooms were maintained on a 12 h light-dark cycle, at an air temperature of 23 C, and a humidity of 55%. The mice were 65-75 days old at the time of irradiation and weighed 24-29 g.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOGEN (Wako pure chemical) + RNeasy (QIAGEN)
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Linear Amplification Kit
|
| |
|
| Channel 2 |
| Source name |
bone marrow, X-ray irradiation, Zn-yeast administration, 6 hours
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeSlc
gender: male
age: 10 weeks
tissue: bone marrow
irradiation: whole body irradiation
treatment: Zn-yeast
|
| Treatment protocol |
The zinc-containing yeast powder was suspended in a 0.5% methylcellulose solution. The suspension (0.3 ml of 8.5 mg/ml = 100 mg/kg) was administered i.p. to C3H mice immediately after 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after irradiation, the bone marrow was flushed from femora and was collected into centrifuge tubes.
|
| Growth protocol |
The mice, received at 8 weeks of age, were housed five per cage and allowed free access to a commercial diet (MB-1, Funabashi Farm Co., Funabashi, Japan) and acidified water during the experimental period. The animal rooms were maintained on a 12 h light-dark cycle, at an air temperature of 23 C, and a humidity of 55%. The mice were 65-75 days old at the time of irradiation and weighed 24-29 g.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOGEN (Wako pure chemical) + RNeasy (QIAGEN)
|
| Label |
Cy3
|
| Label protocol |
Agilent Low RNA Input 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 9.5).
|
| Description |
X-ray irradiated, methylcellulose (Cy5) vs. X-ray irradiated, Zn-yeast (Cy3).
|
| 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 |
Mar 19, 2009 |
| Last update date |
Sep 27, 2010 |
| 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) |
| GSE18727 |
Gene expression profile of bone marrow with post-irradiation radioprotector |
|
| 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 |
