Transcriptomics

Dataset Information

3

Transcription profiling by array of rat retina after intra-orbital nerve transection, intra-orbital nerve crush or no treatment


ABSTRACT: Array experiment: Animals were divided into a control group (naive), which did not undergo any experimental manipulation (n=20) and two experimental groups, one receiving an intra-orbital nerve transection (IONT, n=60) and the other an intra-orbital nerve crush (IONC, n=60) Sterile precautions were maintained for all surgical procedures. The left ON was intraorbitally axotomized according to procedures that are standard in our laboratory. (REF) Briefly, an incision was made in the superior orbital rim, the superoexternal orbital contents were dissected, and the superior and external rectus muscles were removed. When performing IONT, the dura mater was opened longitudinally to spare the blood supply, and the optic nerve was transected 0.5 mm from the optic disc. To perform IONC the optic nerve was crushed 3 mm from the optic disc during 10 seconds using a pair of watchmakerÌÄåâÌâåÕs forceps (Vidal-Sanz et al., 1988, 1991; Villegas-PÌÄåÄÌâå©rez et al., 1993). Before and after the procedure, the eye fundus was observed through the operating microscope to assess the integrity of the retinal blood flow. Tissue processing and RNA extraction: Animals were kept the appropriate time post injury (12h, 24h, 48h, 3d 7d and 15d, n=8-12 per time point) and then sacrificed by an intraperitoneal overdose of sodium pentobarbital. Left retinas were fresh dissected and immediately frozen in liquid nitrogen. Four retinas from each time point, animal group and biological replica were pooled and RNA was extracted using Trizol (Invitrogen). RNA was further cleaned through RNAeasy mini kit columns (Quiagen). The RNA integrity was checked using a Bioanalyzer (Agilent Technologies, USA) and concentrations were determined using a NanoDrop (NanoDrop Technologies, Wilmington, DE, USA).

REANALYSED by: E-MEXP-1387

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Rattus norvegicus  

SUBMITTER: Marta Agudo  

PROVIDER: E-MEXP-1387 | ArrayExpress | 2008-06-14

REPOSITORIES: ArrayExpress

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Publications

Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush.

Agudo Marta M   Pérez-Marín Maria Cruz MC   Lönngren Ulrika U   Sobrado Paloma P   Conesa Ana A   Cánovas Isabel I   Salinas-Navarro Manuel M   Miralles-Imperial Jaime J   Hallböök Finn F   Vidal-Sanz Manuel M  

Molecular vision 20080603


PURPOSE: A time-course analysis of gene regulation in the adult rat retina after intraorbital nerve crush (IONC) and intraorbital nerve transection (IONT). METHODS: RNA was extracted from adult rat retinas undergoing either IONT or IONC at increasing times post-lesion. Affymetrix RAE230.2 arrays were hybridized and analyzed. Statistically regulated genes were annotated and functionally clustered. Arrays were validated by means of quantative reverse transcription polymerase chain reaction (qRT-PC  ...[more]

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