|
| Status |
Public on Feb 01, 2010 |
| Title |
SHAM eye at 21 days post-ONX, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
SHAM eye at 21 days post-ONX, biological replicate 1
|
| Organism |
Danio rerio |
| Characteristics |
tissue: eye
|
| Treatment protocol |
For optic nerve crush fish were anesthetized by immersion in 0.033% aminobenzoic acid ethylmethylester (MS222). The left optic nerve was exposed by gently pulling the eye out of the orbit and then crushing the nerve with forceps. The eye was then gently replaced in the orbit. As a SHAM control the right eye of the same fish was gently pulled out of the orbit and replaced with the nerve remaining intact. The fish were then placed in a recovery tank. At timed intervals post-crush (6 hours and 1, 4, 12, & 21 days) the fish were euthanized by overdose of MS-222 and the eyes (including retina, lens, vitreous, anterior and posterior segments) removed, flash-frozen on dry ice and stored at -70°C. For microarray analysis two biological replicates (2 pools with 5 eyes/pool for each time point) were prepared.
|
| Growth protocol |
Wild type adult male Danio rerio were maintained in 30 gal aquaria at 28ºC on a 14:10 light-dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions and RNA was cleaned using Qiagen RNA clean-up protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
whole eye after sham surgery
|
| 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. The trimmed mean target intensity of each array was arbitrarily set to 100.
|
| |
|
| Submission date |
Dec 03, 2009 |
| Last update date |
Dec 03, 2009 |
| Contact name |
Amy T McCurley |
| Organization name |
Boston University
|
| Department |
Biology
|
| Street address |
5 Cummington Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE19298 |
Gene expression timecourse in zebrafish whole eye in response to optic nerve crush |
|
