|
| Status |
Public on Apr 08, 2010 |
| Title |
control.sup.2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse retina, under normoxia condition, superior half
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: Control (normoxia)
tissue: superior retina
|
| Treatment protocol |
At the age of P (postnatal) 83-90, some mice were exposed to constant hyperoxia (75% O2) for 14 days. Oxygen-exposed animals were euthanized at the end of the period of hyperoxia; controls were euthanized at the same age. Retinas were removed and divided into superior and inferior halves. Retinal samples from 2 animals (1 male and 1 female) were pooled for each condition.
|
| Growth protocol |
C57BL/6J mice, a hyperoxia-vulnerable strain , were used for this study. Mice were raised in dim cyclic illumination (12 hr 5 lux, 12 hr dark) and maintained in this level of lighting during the period of experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using a combination of TRIzol Reagent (Invitrogen™ life technologies, Carlsbad, CA) and RNAqueous-micro kit (Ambion, Foster City, CA). TRIzol was used to isolate the RNA and the RNAqueous kit was used to purify and DNase-treat the RNA.
|
| Label |
biotin
|
| Label protocol |
Staining, hybridization, washing and scanning of the array were performed at the Biomolecular Resource Facility at the John Curtin School of Medical Research, Australian National University, following manufacturers’ protocols. Biotinylated sense-strand DNA targets from the entire expressed genome were prepared from 100ng total RNA, according to the Affymetrix Whole Transcript (WT) Sense Target labeling Assay Manual.
|
| |
|
| Hybridization protocol |
7.5 ug of fragmented and labeled DNA target were used. Heat hybridization mixture at 99ْC for 5 mins (in lab heat block), then cool to 45ْC (in lab heat block) for 5 mins and centrifuge at max speed for 5 min. Inject approx 100uL of sample into array. Tough Spot the holes over the septa and immediately place the array in 45ْC hybridization oven at 60rpm for 17hours. Arrays were washed and stained in the Fluidics Station using the Prime_450 protocol.
|
| Scan protocol |
Arrays were scanned using the Affymetrix Launcher. For Mouse, use MoGene 1_0-st-v1 universal Module and the FS450_0007 fluidics protocol.
|
| Description |
mouse retina, under normoxia condition, superior half, rep 2
|
| Data processing |
CEL files were imported into Partek Genomics Suite, with the following normalization of their configuration: Probes to import - interrogating probes; Probe filtering - include core; Background correction - RMA background; Log base - 2; Probeset summarization - Median Polish.
|
| |
|
| Submission date |
Apr 07, 2010 |
| Last update date |
Apr 07, 2010 |
| Contact name |
Yuan Zhu |
| E-mail(s) |
yuan.zhu@anu.edu.au
|
| Phone |
+61 2 61254489
|
| Organization name |
Australian National University
|
| Department |
Research School of Biology
|
| Street address |
Bldg 46, RSBS, ANU
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE21246 |
Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia |
|
