Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray

Ken A. Morris, Einat Snir, Celine Pompeia, Irina V. Koroleva, Bechara Kachar, Yoshihide Hayashizaki, Piero Carninci, M. Bento Soares, Kirk Beisel

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Microarray analyses have contributed greatly to the rapid understanding of functional genomics through the identification of gene networks as well as gene discovery. To facilitate functional genomics of the inner ear, we have developed a mouse inner-ear-pertinent custom microarray chip (CMA-IE1). Nonredundant cDNA clones were obtained from two cDNA library resources: the RIKEN subtracted inner ear set and the NIH organ of Corti library. At least 2000 cDNAs unique to the inner ear were present on the chip. Comparisons were performed to examine the relative expression levels of these unique cDNAs within the organ of Corti, lateral wall, and spiral ganglion. Total RNA samples were obtained from the three cochlear-dissected fractions from adult CF-1 mice. The total RNA was linearly amplified, and a dendrimer-based system was utilized to enhance the hybridization signal. Differentially expressed genes were verified by comparison to known gene expression patterns in the cochlea or by correlation with genes and gene families deduced to be present in the three tissue types. Approximately 22-25% of the genes on the array had significant levels of expression. A number of differentially expressed genes were detected in each tissue fraction. These included genes with known functional roles, hypothetical genes, and various unknown or uncharacterized genes. Four of the differentially expressed genes found in the organ of Corti are linked to deafness loci. None of these are hypothetical or unknown genes.

Original languageEnglish
Pages (from-to)75-89
Number of pages15
JournalJARO - Journal of the Association for Research in Otolaryngology
Volume6
Issue number1
DOIs
StatePublished - Mar 2005

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Cochlea
Inner Ear
Gene Expression
Genes
Organ of Corti
Complementary DNA
Genomics
RNA
Spiral Ganglion
Dendrimers
Gene Regulatory Networks
Genetic Association Studies
Deafness
Microarray Analysis
Gene Library
Clone Cells

All Science Journal Classification (ASJC) codes

  • Otorhinolaryngology
  • Physiology

Cite this

Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. / Morris, Ken A.; Snir, Einat; Pompeia, Celine; Koroleva, Irina V.; Kachar, Bechara; Hayashizaki, Yoshihide; Carninci, Piero; Soares, M. Bento; Beisel, Kirk.

In: JARO - Journal of the Association for Research in Otolaryngology, Vol. 6, No. 1, 03.2005, p. 75-89.

Research output: Contribution to journalArticle

Morris, Ken A. ; Snir, Einat ; Pompeia, Celine ; Koroleva, Irina V. ; Kachar, Bechara ; Hayashizaki, Yoshihide ; Carninci, Piero ; Soares, M. Bento ; Beisel, Kirk. / Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. In: JARO - Journal of the Association for Research in Otolaryngology. 2005 ; Vol. 6, No. 1. pp. 75-89.
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