|
| Status |
Public on Dec 03, 2016 |
| Title |
Dex12h |
| Sample type |
RNA |
| |
|
| Source name |
Cochlear tissue 12h after noise and dexamethasone administration
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cochlea
gender: female
age: 6weeks
stress: noise
treatment: dexamethasone
time: 12h
|
| Treatment protocol |
Mice were exposed to intense noise for 2h. Immediately following noise exposure, dexamethasone sodium triphosphate (10mg/kg) or control saline was intraperitoneally injected. At 12 and 24h following the noise exposure and dexamethasone administration, mice were deeply anesthetized and the cochlear tissue was dissected in RNA later (Qian, Valencia, CA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using miReasy column (Qiagen) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.１ ug RNA using the One-Color Low Input Quick amp labeling kit (Agilent, Santa Clara, CA) 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 and Agilent 2100 Bioanalyzer.
|
| |
|
| 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 following the manufacturer’s instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Microarray ver 2 (G4853B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash buffer 2 (Agilent), then dried immediately.
|
| Scan protocol |
Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were quantified using Feature Extraction 10.10.1.1 software (Agilent). The data was analyzed with GeneSpring GX software. 14.5.0 (Agilent). Using GeneSpringGX, intensity of each probe was normalized to 75th percentile with no baseline transformation, and represented the expression levels of each genes.
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
Dec 03, 2016 |
| Contact name |
Yukihide Maeda |
| E-mail(s) |
yamayuki@cc.okayama-u.ac.jp
|
| Phone |
81862357307
|
| Organization name |
Okayama University Hospital
|
| Department |
Department of Otolaryngology-, Head and Neck Surgery
|
| Street address |
2-5-1 Shikata, Kita-Ku
|
| City |
Okayama |
| ZIP/Postal code |
700-8558 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE85290 |
Cochlear transcriptome after noise trauma and dexamethasone therapy in mice |
|
