|
| Status |
Public on Jun 05, 2018 |
| Title |
retina/RPE/choroid_FD_24hr_pooled |
| Sample type |
RNA |
| |
|
| Source name |
retina/RPE/choroid_FD_24hr
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Leghorn/New Hampshire
gender: male
treatment: 7 days form deprivation (FDM)
post-treatment: 24 hours recovery
age: Post-hatch day 12
time-point: 8 days (post-occlusion)
lens type: FDMR (24hrs)
tissue: Retina, RPE, choroid
|
| Treatment protocol |
Male chicks (Leghorn/New Hampshire) were raised from post-hatch days 0-2 under a 12-hr day/night light cycle in groups of <25. In the middle of the light cycle on day 2, chicks were randomly assigned to a lens condition (FD or No Lens) and occluders attached to Velcro were fixed to the periocular feathers of the right eye. Following a further 10 days, tissue was collected from no lens and FDM chicks. At the same time, occluders were removed from FDMR chicks. Tissue was collected from these FDMR chicks following 6hrs or 24hrs recovery.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the SV total RNA isolation system (Promega Australia, NSW), including DNA digestion. The quality of the RNA samples was assessed via NanoDrop® ND-1000 Spectrophotometer and found to fall within the acceptable absorbance (260/280) range of 1.8-2.1.
|
| 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).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneArray Scanner GS3000.
|
| Description |
After initiation of form deprivation myopia (FDM) for 7 days, occluders were removed to allow 24hrs of normal light and FDM recovery (FDMR)
FD_24hrs
|
| Data processing |
To determine present/absent calls, raw data was analyzed with Expression Console using MAS5 using default analysis settings. To determine expression values, raw data was analyzed with Expression Console using RMA using default analysis settings.
|
| |
|
| Submission date |
Oct 31, 2016 |
| Last update date |
Jun 05, 2018 |
| Contact name |
Loretta Giummarra |
| E-mail(s) |
L.Giummarra@latrobe.edu.au
|
| Organization name |
La Trobe University
|
| Department |
Psychology & Counselling
|
| Street address |
c/o Psychological Science
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3086 |
| Country |
Australia |
| |
|
| Platform ID |
GPL3213 |
| Series (1) |
| GSE89325 |
Pathway analysis identifies altered mitochondrial metabolism, neurotransmission, structural pathways and complement cascade in retina/RPE/choroid in chick model of form-deprivation myopia |
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