|
| Status |
Public on Jul 16, 2010 |
| Title |
Rat retina_PBM + Light Damage_ rep1 |
| Sample type |
RNA |
| |
|
| Source name |
retina, pretreatment PBM, 3mins each day for 5 days, 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 exposed to 670nm red light from a WARP 75 source (Quantum Devices Inc, Barneveld, WI, USA). Animals were handled gently over several days until they were adapted to handling, Each was then gently restrained with a towel and held under a plexiglass platform with the head ~2.5cm below the platform. The WARP75 device was placed on top of the platform and turned on for 3 min. This arrangement provided a fluence of10J/cm2 at the eye. The animals did not hide from or appear agitated by the red light. Animals were treated in this way once daily for 5 days, at 9.00 am. Tissue was collected 24h after the last treatment.
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.).
|
| |
|
| 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 PBM (5 days for 3mins) 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) |
[email protected]
|
| 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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