|
| Status |
Public on Aug 11, 2011 |
| Title |
chicken eye, +15 diopter lens, 3 days, biological replicate 5_Chicken_437e |
| Sample type |
RNA |
| |
|
| Source name |
retina/RPE, +15 diopter lens, 3 days
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: retina/RPE
breed: White Leghorn
age: less than 2 weeks
|
| Treatment protocol |
At one week of age, either a (+) or a (-) 15 diopter lens was adhered to one eye of each chick for a period of either 6 hours or 3 days.
|
| Growth protocol |
One day old chicks were maintained under a 12 hour light:dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol/Rneasy extraction of total RNA was performed according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Fragmented, biotinylated cDNA was prepared from 100ng of total RNA according to the Nugen Ovation Kit protocol.
|
| |
|
| Hybridization protocol |
3.75ug of labeled cDNA were hybridized to an Affymetrix Chicken Genome Array for 16 hours at 45°C. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Gene Chips were scanned using the Affymetrix 7G Scanner.
|
| Description |
Gene expression data from contralateral eye, (+) lens, 3 days
|
| Data processing |
Affymetrix Command Console was used to quantify expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. CEL files were imported into Partek Genomic Suite(v.6.4) where RMA was applied yielding normalized, log2 transformed signal intensities. All resultiing p-values were corrected for multiple comparisons using the Benjamini-Hochberg step-up method to yield False Discovery Rates (FDR) as implemented in Partek. An FDR of <10% was considered significant
|
| |
|
| Submission date |
Oct 12, 2010 |
| Last update date |
Aug 13, 2011 |
| Contact name |
Alice M McGlinn |
| E-mail(s) |
[email protected]
|
| Phone |
215-898-6508
|
| Fax |
215-898-0528
|
| Organization name |
University of Pennsylvania School of Medicine
|
| Department |
Ophthalmology
|
| Lab |
Dr Richard Stone
|
| Street address |
602D Richards Building 3700 Hamilton Walk
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-6075 |
| Country |
USA |
| |
|
| Platform ID |
GPL3213 |
| Series (1) |
| GSE24641 |
Image defocus and altered retinal gene expression in chicks |
|
