Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 8
Release date: Aug 20 2009
Last update date: Dec 21 2016
Access: Public
Diseases: Ocular Hypertension, Tooth Loss
Dataset link Proteomics and transcriptomics analysis of rat retinal ganglion cells exposed to chronic ocular hypertension.

Experimental Protocol


We performed high-content analyses of molecular changes in retinal ganglion cells associated with chronic ocular hypertension (COH). Gene expression profiling was performed using two-color microarrays. To assess differences in the gene expression levels in COH-challenged vs. normotensive RGCs, the “glaucomatous RGC/ reference RNA” ratios were divided by the ratios of “normotensive RGCs /reference RNA” obtained from the same group of experimental animals. Equivalent amounts of reference and experimental aRNAs were hybridized with the Agilent Rat Oligo Microarrays (Agilent, USA) according to the manufacturer’s instructions. Each microarray was scanned and normalized for signal intensities across the whole array and locally, using the Lowess normalization. We analyzed only those genes that passed Agilent quality control criteria. To reveal the genes with significant changes in glaucoma, we first calculated ratios of expression levels in experimental vs. fellow control eyes for each of four independent groups, and then selected genes with consistent changes using ANOVA and the cut-off p-value <0.05. Within each group, experimental and control RNA was extracted from RGCs purified from eye pairs originating from the same animal. Within each pair, as well as within each pooled group, total RNA abundances were, therefore, normalized for individual differences, so as were the resultant gene expression ratios. A fold change difference ≥1.5 was used to determine differentially expressed genes.

Repositories


GEO

GSE15332

BioProject

PRJNA116561

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Contact


Dmitry Ivanov