|
| Status |
Public on Feb 19, 2010 |
| Title |
Whole retina LA repicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
whole retina; light adapted
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina whole retina
treatment: light adapted
|
| Treatment protocol |
Animals were light adapted for 6h or dark adapted for 3h
|
| Growth protocol |
Adult 7-8 weeks old C57BL/6 mice bred in a pathogen-free environment with ad libitum access to food and drinking water. LA (light adapted) animals were kept in a room with the light phase (450 lux) from 6:00 am (ZT0) to 6:00 pm (ZT12). For dark adaptation, animals were kept in a dark chamber with maximum of 0.4 lux
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Laser capture microscopy was used to isolate retina cell layers. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the two-cycle target labeling Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Standard Affymetrix procedures
|
| Description |
light adapted for 6h
|
| Data processing |
Quality control and background normalization was performed using Refiner 4.1 from Genedata AG (Basel, Switzerland). Expression value estimates were obtained using the GC-RMA implementation in Refiner 4.1. Quantile-normalization and median scaling of the genes called present (detection p value <0.05) was performed in Genedata’s Analyst 4.1 package. Data analysis was performed using Expressionist Analyst 4.1 from Genedata AG. Genes were required to pass a t-test (1-way ANOVA) with a p < 0.05.
|
| |
|
| Submission date |
Feb 17, 2010 |
| Last update date |
Feb 18, 2010 |
| Contact name |
Jacek Krol |
| E-mail(s) |
jacek.krol@fmi.ch
|
| Phone |
00-41-61-6974128
|
| Fax |
00-41-61-6973976
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Department |
Epigenetics
|
| Lab |
W. Filipowicz Group
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE20396 |
Expression data of LCM-dissected retina layers |
|
