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Gene-Expression Analysis for CodeLink Whole Human Genome
Microarray
Using Olfactory Neuroepithelium-Derived Progenitors
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The long-term goal of this study is to develop a database for discovery of genes associated with the human neural progenitors isolated from olfactory mucosa. Eventually, the database will be used for gene target and gene-network determination. The olfactory neurosensory epithelium (One) is a specialized tissue that lines a region of the nasal cavity high in the nasal vault, characterized by its life-long regenerative capacity. ONe progenitors were obtained from frozen stock of previously isolated neurosphere forming cells (NSFCs) that were generated from tissue obtained 8 hr postmortem from a 95yr old female. The total RNA was isolated from p14 (young), p78 (intermediate), and p189 (old) passages (approximately 2 yrs in vitro) and labeled. Ten μg of the labeled and fragmented cRNA for each of these passages was hybridized with three independent gene-microarrays. The data were collected, normalized and log transformed. The reproducibility among technical replicates was determined by different methods including ANOVA, Box plots, scatter plots, and correlation coefficients. Following normalization and data-filtering, the genes which were consistently detectable among the 3 biological samples were declared a common set. Subsequently, the differentially expressed genes in the three biological samples were highlighted based on analysis with the Student’s t-test. Volcano plots were used to determine genes in the common set whose variable expression values between the 3 biological samples were statistically significant. Data analysis of the 7115 transcripts in the common set indicates that about 30 genes in the intermediate passage were differentially expressed relative to the young passage (significance cutoff p-value <0.001), and 67 genes in the old passage were changed relative to the young passage (p-value <0.001). The quantitative RT-PCR method was used to validate some of the expression values detected in the arrays. These data will serve as a basis for future studies of human ONe-derived cell lines. |
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Khalyfa A.1, Qiang H. 2, Xu, M3, Marshall
C.T1 ,Roisen F.J.1, Klueber, K.M.1 and Cooper, N.G.F.
Department of Anatomical
Sciences and Neurobiology 1 ,
Department of Biochemistry and Molecular Biology 2,
University of Louisville School of Medicine, Louisville, Kentucky.
GE
HealthCare3, (Microarray Applications Development, Piscataway, NJ)