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| Status |
Public on Dec 31, 2017 |
| Title |
(c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 7 |
| Sample type |
RNA |
| |
|
| Source name |
Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections)
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6C3F1
gender: Female
disease state: HCA
treatment: irradiated
tissue: liver (adenoma section)
|
| Treatment protocol |
Female B6C3F1 mice from 8 weeks of age were irradiated for 400 d at LDR at 0.02 Gy/22 h/d (0.00091 Gy/h) 137Cs-γ rays (74 GBq), in which the total doses was 8 Gy. And the chronically irradiated mice for 400 d (8 Gy) were bled in the SPF condition without irradiation for 100, 200 and 300 d, in which the total days were 500, 600, 700 d after beginning of irradiation, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A piece of livers with adenomas or non-adenoma were homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) reagent within 2 h after death.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides, (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
(c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 7
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 13.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Jun 14, 2016 |
| Last update date |
Dec 31, 2017 |
| Contact name |
Takashi Sugihara |
| E-mail(s) |
sugihara@ies.or.jp
|
| Organization name |
Institute for Environmental Sciences
|
| Department |
Radiobiology
|
| Street address |
2-121 Hacchazawa
|
| City |
Rokkasho |
| State/province |
Aomori |
| ZIP/Postal code |
039-3213 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE83318 |
Gene expressions of mice hepatocellular adenoma, which correlated with low-dose-rate gamma ray radiation dependent inflammatory response |
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