|
| Status |
Public on Apr 15, 2015 |
| Title |
Mouse cochlea of 12 weeks of age with control vehicle #5 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse cochlea of 12 weeks of age
|
| Organism |
Mus musculus |
| Characteristics |
age: 12 weeks of age
Sex: male
tissue: cochlea
strain: DBA/2J
|
| Treatment protocol |
DBA/2J mice (4 weeks old) were injected subcutaneously once daily for 8 weeks with L-methionine (500 mg/kg) and valproic acid (300 mg/kg) in 0.1M sodium bicarbonate.
|
| Growth protocol |
Mice were housed in plastic cages with metallic lid in a room with a 12-h light/dark cycle and 55% humidity at 23 C and had free access to food and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mouse whole cochlea using TRIzol regent (LifeTechnologies). Additionally, total RNA was purified using Rneasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 3000 7G.
|
| Data processing |
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).
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| |
|
| Submission date |
Oct 08, 2014 |
| Last update date |
Apr 15, 2015 |
| Contact name |
Fuyuki Miya |
| E-mail(s) |
fmiya@keio.jp
|
| Phone |
+81-3-5363-3890
|
| Organization name |
Keio University
|
| Department |
School of Medicine
|
| Lab |
Center for Medical Genetics
|
| Street address |
35 Shinanomachi, Shinjuku-ku
|
| City |
Tokyo |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE62173 |
Expression data of mice cochlea treated with L-methionine and valproic acid. |
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