|
| Status |
Public on Jun 26, 2017 |
| Title |
1w_24h_male1 |
| Sample type |
RNA |
| |
|
| Source name |
1w_24h_male1
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
tissue: liver
age: 1 week-old
|
| Treatment protocol |
B6C3F1 mice were either sham-irradiated, or irradiated at 1 or 7 weeks of age with 4 Gy gamma rays from a 137Cs source (0.57 Gy/min). Liver tissue from irradiated mice was sampled up to 48 h post-irradiation,
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the AllPrep DNA/RNA/Protein Mini kit (QIAGEN) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in 1-week-old mouse liver at 24 hour after 4 Gy Gamma-ray irradiation
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jul 05, 2016 |
| Last update date |
Jun 26, 2017 |
| Contact name |
Kazuhiro DAINO |
| E-mail(s) |
daino.kazuhiro@qst.go.jp
|
| Organization name |
National Institutes for Quantum and Radiological Science and Technology
|
| Street address |
4-9-1 Anagawa, Inage-ku
|
| City |
Chiba |
| ZIP/Postal code |
263-8555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE84041 |
Age-Related Gene Expression in mouse liver tissues after exposure to Gamma-ray irradiation |
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