|
| Status |
Public on Jul 16, 2010 |
| Title |
Rat retina_Saffron + Light Damage_ rep2 |
| Sample type |
RNA |
| |
|
| Source name |
retina, pretreatment saffron then exposued to 24hrs 1000lux light, followed by 1000 lux light for 24hrs.
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: retina
developmental stage: Adult P80 - 120
|
| Treatment protocol |
Animals were fed saffron at 1mg/kg/day, for 3w. Saffron (stigmata of Crocus sativus, from the Abbruzzo region in Italy) was soaked in water (at 2mg of spice/ml H2O) and 12h was allowed for the major anti-oxidants, which are water-soluble, to dissolve fully. The solute was then fed to the rats injecting a small volume into a piece of the vegetable matrix, which the animal readily ingested. The volume for each daily feed was calculated to provide the solutes from 1mg of saffron/kg body weight. Tissue was collected 24h after the last feed.
The animals were kept individually in plexiglass cages, with food kept on the floor of the cages and water offered from transparent containers, to ensure uniform exposure. After overnight dark adaptation, animals were exposed to bright (1000 lux) light for 24h, from a white fluorescent source. Exposure began and ended at 9.00am.
|
| Growth protocol |
All animals were raised in 5 lux cyclic light. They were routinely fed a vegetable (potato or rice) matrix, developed as a biodegradable packaging material, and we used the same matrix used as vehicle for feeding them with saffron.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.
|
| Label |
Biotin
|
| Label protocol |
Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay 2009, Affymetrix, Inc.).
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| |
|
| Hybridization protocol |
Standard Affymetrix protocols were followed in the hybridisation, blocking and washing (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)).
|
| Scan protocol |
Image analysis was performed using the standard Affymetrix protocols (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)). Scanning was performed using the GeneChip® Scanner 3000 and Affymetrix® GeneChip® Command Console® (AGCC).
|
| Description |
Gene expression data from rat retina, pretreated with saffron (3 weeks of 1mg/kg/day) prior to light damage (1000lux for 24 hrs.).
|
| Data processing |
RMA expression values, log transformed (base 2) using Expression console (version 1.1.2800.19935). Normalized data were analyzed using GeneSpring GX v10 software.
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| |
|
| Submission date |
Jul 08, 2010 |
| Last update date |
Jul 15, 2010 |
| Contact name |
Riccardo Natoli |
| E-mail(s) |
riccardo.natoli@anu.edu.au
|
| Phone |
+ 61 2 6125 8559
|
| Fax |
+ 61 2 6125 8680
|
| Organization name |
ANU
|
| Department |
CMBE
|
| Lab |
Provis Lab
|
| Street address |
Sullivans Creek Road
|
| City |
Acton |
| State/province |
ACT |
| ZIP/Postal code |
2617 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE22818 |
Comparison of Saffron and Photobiomodulation on the light damaged rat retina. |
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