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| Status |
Public on Jun 06, 2014 |
| Title |
ATRA [2d] |
| Sample type |
RNA |
| |
|
| Source name |
liver_ATRA_2 days
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
gender: male
genotype/variation: wild type
treated with: all-trans-retinoic acid (ATRA)
time point: 2 days after treatment
tissue: liver
|
| Treatment protocol |
DEN (Tokyo Chemical Industry, Tokyo, Japan) was administered in the drinking water (80 mg/L) at approximately 400 µg/day. ATRA (Wako Pure Chemical Industries, Osaka, Japan) was dissolved in ethanol and dimethyl sulfoxide and administered in the drinking water (30 mg/L) at approximately 150 µg/day or in the culture medium. As a control, the vehicle-treated group was administered water. On the day before DEN treatment, G0s2 siRNA or control siRNA (1.6 nmol) was administered to mice intravenously using LipoTrust EX Oligo in vivo (Hokkaido System Science, Sapporo, Japan).
Genes induced by the following treatment in mice liver were investigated at 2 days after treatment;
DEN: diethylnitrosamine (treatment of DEN (drinking water 80 mg/L))
ATRA: retinoic acid (treatment of ATRA (drinking water 30 mg/L))
G0s2 siRNA : G0s2 knockdown mouse liver (treatment of G0s2 siRNA)
Control siRNA: treatment of scramble siRNA (negative control)
|
| Growth protocol |
Male ICR mice (5 weeks old) were purchased from Kyudo Co. Ltd. (Tosu, Japan). Mice were housed in a light-controlled room (lights on from 07:00 to 19:00) at 24 ± 1°C and 60 ± 10% humidity with food and water ad libitum. The animals were adapted to the environmental conditions for 1 week before the experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
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| |
|
| Hybridization protocol |
cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Description |
SAMPLE 2
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensitieswere log2-transformed and normalized by the quantile algorithm with the Bioconductor. Then the normalized data were converted to linear scale ('un-log2-transormed') for intuitive readability.
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| |
|
| Submission date |
May 19, 2014 |
| Last update date |
Jun 06, 2014 |
| Contact name |
naoya matsunaga |
| E-mail(s) |
matunaga@phar.kyushu-u.ac.jp
|
| Organization name |
kyushu university
|
| Street address |
maidashi 3-1-1, higashi-ku
|
| City |
fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
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