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| Status |
Public on Dec 25, 2009 |
| Title |
Differential gene expression in Danio rerio during optic nerve regeneration |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
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| Summary |
To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted. Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression.
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| Overall design |
Wild type zebrafish were obtained from a local pet store. Optic nerve injury was conducted using a severing model accomplished as follows. Zebrafish were anesthetized in 0.2% MS-222 dissolved in tank water. The muscles surrounding the eye were cut and the eye angled rostrally to expose the nerve. The optic nerve was then severed using microsissors without damaging the ophthalmic artery. In sham operated fish the muscles surrounding the eye were severed but the nerve was not damaged. RNA was extracted from the eye at three time points following surgery 3 hours, 24 hours, and 168 hours. RNA was pooled from multiple fish to achieve 10 ug total RNA. Samples were collected in triplicate per time point. Gene expression was analyzed on a dual color oligonucleotide array where the optic nerve injured fish were compared to sham-operated fish. Four samples of RNA were also collected from control fish and compared to each other on the microarray to confirm that processing did not create expression differences.
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| Contributor(s) |
Saul KE, Koke JR, Garcia DM |
| Citation(s) |
19896551 |
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| Submission date |
Aug 27, 2009 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Dana M Garcia |
| E-mail(s) |
dg08@txstate.edu
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| Phone |
512-245-3368
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| Fax |
512-245-8713
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| Organization name |
Texas State University-San Marcos
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| Department |
Biology
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| Lab |
Garcia/Koke Lab
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| Street address |
601 University Drive
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| City |
San Marcos |
| State/province |
TX |
| ZIP/Postal code |
78666 |
| Country |
USA |
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| Platforms (1) |
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| Samples (4)
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| GSM445919 |
zebrafish eye_control replicate1,2,3,4 |
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| Relations |
| BioProject |
PRJNA120093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE17854_RAW.tar |
12.9 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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