|
| Status |
Public on Jun 14, 2023 |
| Title |
Hepatocyte_nonirradiated_AL_40Weeks, #1 |
| Sample type |
RNA |
| |
|
| Source name |
Hepatocyte_nonirradiated_AL_40Weeks
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hepatocyte
treatment: nonirradiated_AL
time: 40 weeks
|
| Treatment protocol |
Mice were left untreated or were subjected to whole-body X-ray-irradiation (3.8 Gy, 0.6 Gy/min) at 1 week of age, then sampling at 7, 8, 10, and 40 weeks.
|
| Growth protocol |
Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (MB-1; Funabashi Farm, Chiba, Japan) until 7-week-old, then changed to AL (95kcal/mouse/week) diet and CR (65kcal/mouse/week) diet (Funabashi Farm, Chiba, Japan), and sterilized water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input 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 |
0.6 ug of Cy3-labelled cRNA (specific activity >6.0 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 Rat GE 8x60K Microarray 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 (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in 40Weeks nonirradiated AL hepatocyte
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20120224). Signal intensity data were normalized using Lowess normalization. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 03, 2021 |
| Last update date |
Jun 14, 2023 |
| Contact name |
Kazuhiro DAINO |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE176108 |
Effect of childhood ionizing radiation exposure and calorie restriction on NASH-like pathological disorder induction and hepatocellular carcinoma development in mouse model |
|
