|
| Status |
Public on Nov 04, 2005 |
| Title |
retina_DBA_1025L_3mo_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Animal id 1025, left retina, 3 months, female, DBA/2J
|
| Organism |
Mus musculus |
| Characteristics |
Age: 3 months, Sex: Female, Retina: left, Final IOP (mm Hg): 15.3, Strain:DBA/2J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole retinas were removed from 3, and 8 month old DBA/2J mice and rinsed in ice-cold 0.1 M phosphate buffered saline to remove blood. Three individual retinas at each age were homogenized in Qiagen RLT buffer using a micro pestle and pulled five times through a 22G needle, then flash frozen in liquid nitrogen.
|
| Label |
biotin
|
| Label protocol |
Total RNA was isolated using a Qiagen RNeasy Kit. The quantity and quality of the RNA was assessed using a Nanodrop ND1000 spectrophotometer and an Agilent 2100 Bioanalyzer. 20ng of each retinal RNA sample was amplified, fractionated, and labeled with a NuGEN Ovation Biotin kit to generate probe for Affymetrix microarray analysis.
|
| |
|
| Hybridization protocol |
standard Affymetrix procedures
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
Three month old female DBA/2J mouse retina
|
| Data processing |
All preprocessing of Affymetrix data was performed using the Bioconductor Package in the R statistical environment. Data set analysis done under the R statistical environment version 1.9.0 on i686-pc-linux-gnu. Bioconductor package 'affy' version 1.4.32, 'gcrma' version 1.1.0, 'siggenes'(R sam analysis) version 1.0.6.
|
| |
|
| Submission date |
Nov 03, 2005 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Monica L. Vetter |
| E-mail(s) |
monica@neuro.utah.edu
|
| Phone |
(801) 581-4984
|
| Organization name |
University of Utah
|
| Department |
Neurobiology & Anatomy
|
| Lab |
Vetter Lab
|
| Street address |
20 South, 2030 East Rm. 320 BPRB
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112-9458 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE3554 |
Microarray Analysis of Retinal Gene Expression in the DBA/2J Model of Glaucoma |
|
| Relations |
| Reanalyzed by |
GSE119085 |
