|
| Status |
Public on Aug 10, 2012 |
| Title |
Muller glia derived progenitors_4 day post injury_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Injured Muller glia derived retinal progenitors, 4 dpi
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: 1016 tuba1a:gfp transgenic (GFP under tuba1a promoter )
age: 7 months old zebrafish retina
tissue: retinas at 4 days post injury
cell type: Muller glia
|
| Treatment protocol |
Fishes were anesthetized using tricaine methane sulfonate prior to retinal injury using a 30G needle from the back of the eye. Each fish received one poke per quadrant of the eye circle. Uninjured fishes were not given any injury. Experiments were done ss per the University of Michigan animal care protocol.
|
| Growth protocol |
Fishes were grown at 14-10 light-dark cycles, fed thrice daily and maintained as per the animal care protocols of University of Michigan.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated Muller glia and Muller glia derived retinal progenitors obtained from zebrafish retina using standard Trizol method.
|
| Label |
Alexa 555
|
| Label protocol |
Alexa 555 labeled cRNA was prepared from 0.7 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions,
|
| |
|
| Hybridization protocol |
1.5 ug of Alexa 555-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent zebrafish (Danio rerio) oligo microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of Injured Muller glia derived retinal progenitors
SAMPLE 3
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 015064_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 01, 2012 |
| Last update date |
Aug 10, 2012 |
| Contact name |
Rajesh Ramachandran |
| E-mail(s) |
rajeshra@umich.edu
|
| Phone |
17349363649
|
| Organization name |
University of Michigan
|
| Department |
Molecular and Behavioral Neuroscience Institute
|
| Lab |
Goldman Lab
|
| Street address |
109 Zina Pitcher Place
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL7302 |
| Series (1) |
| GSE36191 |
Transcriptome analysis of the uninjured Muller glia (MG) and MG derived retinal progenitors at 4 day post injured zebrafish retina |
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