Genes Expressed In The Mouse Cochlea

This is a search engine for genes expressed in the mouse cochlea. The data set consists of results of an Affymetrix 430 2.0 chip analysis of 8 normal CBA/CaJ male 9 week old mice, designated C1-C8. The mice were given an overdose of anesthesia and sterile saline was perfused intracardially to remove blood cells from the ear. The cochleas were removed, placed in RNAlater, and the petrous bone removed with jeweler's forceps to expose the inner ear. All inner ear soft tissue, including the spiral ligament, organ of Corti, and modiolar tissue was collected. The two ears of each animal were pooled to create 8 samples. Total RNA was extracted with TRIZOL. RNA was amplified with Nugen Ovation RNA Amplification System V2. Hybridization was carried out on an Affymetrix Model 640 hybridization chamber. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
The present engine allows one to search for genes by searching for accession number, gene symbol, or gene name. (Partial names may be used.) Many genes have various accession numbers and names. The most often cause of finding no hits of a search is the use of an entry that is not in the Affymetrix list. Web sites that are useful for showing aliases and alternative gene names are iHOP and Gene Cards. Results of searches are displayed in the standard Affymetrix format as P (present at the 95% confidence level), A (absent) and M (ambiguous). The signal strength for mouse C1 is displayed as a rough index of expression level. Signal strengths for the 8 cases were highly correlated and signals as low as approximately 35 usually resulted in "P" scores for all 8 mice. The entire data set has been deposited in NCBI's Gene Expression Omnibus and can be queried or downloaded from there.
Author:
Joe C. Adams, PhD
Harvard Medical School
Massachusetts Eye and Ear Infirmary
243 Charles Street
Boston, MA 02114, USA
joe_adams@meei.harvard.edu

This project was funded by the generosity of Mr. and Mrs. Charles Safford.