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Differential gene expression in Danio rerio during optic nerve regeneration


ABSTRACT: 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. 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.

ORGANISM(S): Danio rerio

SUBMITTER: Joseph Koke 

PROVIDER: E-GEOD-17854 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Activating transcription factor 3 (ATF3) expression in the neural retina and optic nerve of zebrafish during optic nerve regeneration.

Saul Katherine E KE   Koke Joseph R JR   García Dana M DM  

Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 20091105 2


Fish, unlike mammals, can regenerate axons in the optic nerve following optic nerve injury. We hypothesized that using microarray analysis to compare gene expression in fish which had experienced optic nerve lesion to fish which had undergone a similar operation but without optic nerve injury would reveal genes specifically involved in responding to optic nerve injury (including repair), reducing detection of genes involved in the general stress and inflammatory responses. We discovered 120 gene  ...[more]

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