|
| Status |
Public on Nov 30, 2009 |
| Title |
Retina homozygous KO 30 days 2 |
| Sample type |
RNA |
| |
|
| Source name |
Retina, 30 days old homozygous Egr-1 knock-out mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6
gender: male
genotype: Egr-1 knock-out
age: 30 days
tissue: retina
|
| Treatment protocol |
Mice were killed by an overdose of diethylether at the mean age of 30 days (p29-p31) or 42 days (p41-p43). Afterwards, the eyes were enucleated, the retinas were prepared and immediately snap-frozen in liquid nitrogen. The retinas of 12 homozygous Egr-1 knock-out mice (hm) and 12 wildtype mice (wt) of the same strain were prepared for both time points (48 animals in total).
|
| Growth protocol |
Animals were housed in standard cages with their littermates under a 12 hours light/dark cycle with unrestricted access to water and food pellets. Illumination was provided by standard fluorescent lamps and was approximately 200 lux.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three single retinas from different mice were pooled to obtain 4 samples per group (wt30, wt42, hm30, hm42), and RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The quality of total RNA was monitored by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (see manufacturer´s website: Expression Analysis Technical Manual, One-Cycle Target Labeling Assay, Affymetrix).
|
| |
|
| Hybridization protocol |
see manufacturer's website
|
| Scan protocol |
Scanning and analysis were carried out using the Affymetrix Microarray Suite Software (version 5.0)
|
| Description |
RNA sample consists of three separate retinal samples that were pooled
|
| Data processing |
Signal intensities were analyzed using ArrayAssist 4.0 (Stratagene, La Jolla, CA). Transformation algorithm: GC-RMA.
|
| |
|
| Submission date |
Jul 07, 2009 |
| Last update date |
Nov 30, 2009 |
| Contact name |
Marita Pauline Feldkaemper |
| E-mail(s) |
[email protected]
|
| Phone |
+49-7071-2987424
|
| Organization name |
University Eye Hospital Tuebingen, Institute for Ophthalmic Research
|
| Department |
Section of Neurobiology of the Eye
|
| Lab |
Prof. Dr. Frank Schaeffel
|
| Street address |
Calwerstrasse 7/1
|
| City |
Tuebingen |
| ZIP/Postal code |
72074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE16974 |
Retinal gene expression in Egr-1 knock-out mice during development (p30 and p42) |
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