|
| Status |
Public on Jul 16, 2010 |
| Title |
Rat retina_PBM_ rep1 |
| Sample type |
RNA |
| |
|
| Source name |
retina, pretreatment PBM, 3mins each day for 5 days
|
| 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.
|
| 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 exposued to normal light levels and 5 days of 3 mins/day PBM.
|
| 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.
|
| |
|
| 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. |
|
