|
| Status |
Public on Sep 10, 2012 |
| Title |
KO4 |
| Sample type |
RNA |
| |
|
| Source name |
SeBP1 knockout
|
| Organism |
Mus musculus |
| Characteristics |
background/strain: C57BL/6J
genotype/variation: SeBP1 knockout
tissue: ovary
gender: female
age: 20 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (QIAGEN).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg RNA using a One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by purification with an RNeasy column (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked by NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNA (1.5 µg) was fragmented at 60°C for 30 min in a reaction mixture (250 µl) containing 1x fragmentation buffer and 2x blocking agent obtained from Agilent. On completion of the fragmentation reaction, 250 µl 2x Agilent hybridization buffer was added to the mixture, and this mixture was then hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating oven. After hybridization, the microarray slides were washed with GE Wash Buffer 1 (Agilent) for 1 min at room temperature, and with GE Wash buffer 2 (Agilent) for 1 min at 37°C. Immediately after the washing, the slides were dried by centrifugal evaporator.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area, 61x21.6 mm; Scan resolution, 10 um; and Dye channel setting for Green and Green PMT; 100%).
|
| Description |
Replicate 3.
|
| Data processing |
The scanned images were analyzed by Feature Extraction Software (Agilent) using default parameters to subtract background and to obtain processed signal intensities by the algorithm of Spatially Detrend in the software.
|
| |
|
| Submission date |
Mar 21, 2012 |
| Last update date |
Sep 10, 2012 |
| Contact name |
Tomoki Takeda |
| E-mail(s) |
takeda@phar.kyushu-u.ac.jp
|
| Phone |
+81-92-642-6587
|
| Fax |
+81-92-642-6588
|
| Organization name |
Kyushu University
|
| Department |
Pharmaceutical sciences
|
| Lab |
Molecular life sciences
|
| Street address |
3-1-1 Maidashi, Higashi-ku
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE36697 |
Effect of deletion of the selenium-binding protein 1 gene on gene expression in the ovary of C57BL/6J mouse |
|
