|
| Status |
Public on Apr 15, 2011 |
| Title |
D2-Gpnmb+ control rep5 (retina) |
| Sample type |
RNA |
| |
|
| Source name |
Retina no glaucoma
|
| Organism |
Mus musculus |
| Characteristics |
phenotype: no glaucoma
gender: female
strain: D2-Gpnmb+
tissue: retina
age: 10.5 months
|
| Growth protocol |
All mice were housed in a 14 h light to 10 h dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
|
| Scan protocol |
The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner
|
| Description |
Retina R113417
|
| Data processing |
The images were quantified using GeneChipTM Operating Software (GCOS) v1.2. Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package
|
| |
|
| Submission date |
Mar 04, 2011 |
| Last update date |
Apr 15, 2011 |
| Contact name |
Gareth Rhys Howell |
| E-mail(s) |
[email protected]
|
| Phone |
207 288 6572
|
| Fax |
207 288 6078
|
| Organization name |
The Jackson Laboratory
|
| Street address |
600 Main Street
|
| City |
Mount Desert |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE26299 |
Gene expression profiling in DBA/2J glaucoma |
|
