|
| Status |
Public on Feb 24, 2012 |
| Title |
Pooled retinal RNA from room air-exposed post-natal day 5 SD rats, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Retinae, exposed to room air to post-natal day 5
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: retina
treatment: room air-exposed
age: 5d
|
| Treatment protocol |
Within 12 hours of birth, female rats and their litters were placed in a humidified oxygen chamber and exposed to alternating 24 hour cycles of hyperoxia (80% oxygen in air) and normoxia (21% oxygen in air) until the rats were euthansed at post-natal days 5 and 6. Age-matched room air-exposed rats were used as controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the retinae of individual rats using TRIzol according to the manufacturer's method. Total RNA was further purified using a Qiagen Rneasy Micro column purification kit according to the manufacturer's protocol.
|
| Label |
Biotin
|
| Label protocol |
As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix WT cDNA Synthesis and Amplification Kit (Part# 900673) and Affymetrix WT Terminal Labeling and Control Regents (Part# 901524). The rRNA reduction step is not recommended by Affymetrix for the Genearrays and was not performed.
|
| |
|
| Hybridization protocol |
As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Hybridization, Wash and Stain Kit (P/N 900720)
|
| Scan protocol |
As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Scanner 3000 7G
|
| Data processing |
CEL files generated from DAT files automatically by Affymetrix AGCC software. CEL files processed using Partek Genomics Suite v 6.4 using RMA background correction and Partek GC content correction.
|
| |
|
| Submission date |
Feb 23, 2012 |
| Last update date |
Feb 24, 2012 |
| Contact name |
Melinda N Tea |
| E-mail(s) |
melinda.tea@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
Ophthalmology
|
| Lab |
Rm 5D214
|
| Street address |
Flinders Medical Centre, Carpark Building
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE36037 |
Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR). |
|
