|
| Status |
Public on Nov 20, 2013 |
| Title |
300mM 3NP at 3d |
| Sample type |
RNA |
| |
|
| Source name |
Upper basal trun of cochlear lateral wall 3 day after 300mM of 3NP treatment
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: cochlear lateral wall
treatment: 3-NP
time: 3 d
model: acute mitochondrial dysfunction model in the cochlea
strain: Sprague-Dawley
|
| Treatment protocol |
After general anesthesia with pentobarbital (30–40 mg/kg, i.p.) and the local administration of lidocaine (1%), an incision was made posterior to the left pinna near the external meatus. The left otic bulla was opened and the round window niche was infused with 3-NP (500 mM or 300 mM) dissolved in saline (pH adjusted to 7.4 with NaOH). Infusion with saline alone was used as a control. Following treatment, and before the wound was closed, a small piece of gelatin was placed onto the niche to keep the solution in place and to allow for head movement after the animals awoke. The right cochlea was surgically destroyed to avoid cross-hearing during the recording of auditory brain-stem responses. The second turn of the lateral wall (excluding the stria vascularis) was harvested under the dissection microscope.
|
| Growth protocol |
Female Sprague-Dawley rats weighing between 180 g and 210 g (8–10 weeks old) were purchased and bread in a SPF graded clean room.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Expression Array using Affymetrix genechip hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using Molecular Dynamicfs GenePix4000A Lucida Module1(Amersham parmacia biotech Ludica base).
|
| Description |
Gene expression data from upper basal trun of cochlear lateral wall 3 day after 300mM of 3NP treatment
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
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| |
|
| Submission date |
Nov 19, 2013 |
| Last update date |
Nov 20, 2013 |
| Contact name |
Masato Fujioka |
| Organization name |
Keio University School of Med
|
| Department |
Otorhinolaryngology
|
| Street address |
35 Shinanomachi Shinjuku
|
| City |
Tokyo |
| ZIP/Postal code |
1608582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL342 |
| Series (1) |
| GSE52500 |
Gene expression data from rat cochlear lateral wall after 3NP damage |
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