|
| Status |
Public on Apr 26, 2013 |
| Title |
Retina_AAP_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
retina, 7 days
|
| Organism |
Mus musculus |
| Characteristics |
treatment: peptide AAP
gender: male
strain: C57BL/6
tissue: retina
developmental stage: adult
|
| Treatment protocol |
Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.
|
| Growth protocol |
We intravitreally injected 1 μM of PBS, AAP, or HAN into the right eyes of C57BL/6 male mice. One week later, the mice were sacrificed and the eyes were enucleated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).
|
| |
|
| Hybridization protocol |
After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).
|
| Scan protocol |
The hybridized images were scanned using Agilent’s DNA microarray scanner (G2565AA) and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).
|
| Data processing |
All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).
|
| |
|
| Submission date |
Apr 25, 2013 |
| Last update date |
Apr 26, 2013 |
| Contact name |
Jeong Hun Kim |
| Organization name |
Seoul National University
|
| Lab |
FARB (Fight against Angiogenesis-Related Blindness) Laboratory
|
| Street address |
101, Daehak-ro, Jongno-gu
|
| City |
Seoul |
| ZIP/Postal code |
110744 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE46378 |
Investigation of Alterations in Gene Expression in the Retina Induced by High-Affinity Peptides targeting vascular endothelial growth factor, AAP and HAN |
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