E-GEOD-5446 - Transcription profiling of rat organ of Corti (OC), modiolus (MOD) and stria vascularis (SV) of newborns

Status
Submitted on 3 August 2006, released on 13 June 2008, last updated on 27 March 2012
Organism
Rattus norvegicus
Samples (16)
Array (1)
Protocols (19)
Description
The aim of this study was to characterize the basal expression of OC, MOD and SV of newborn rats (3-5 day old) and its changes by short–term cultivation (24 hrs) and mild hypoxia (5 hrs). Three varieties of tissue samples were analyzed (i) Freshly prepared tissue, used as control; (ii) cultures held under normoxic conditions and (iii) cultures exposed during cultivation to 5 h hypoxia. The gene expression was analyzed using the Affymetrix GeneChip RN-U34. The functional specificity of the cochlea regions are well reflected by the gene expression pattern. For example, the basal expression of Organ of Corti is characterized by genes involved in potassium and calcium homeostasis. The MOD is characterized by genes involved in regulation of maturation of neuronal cells. The SV is characterized by genes involved in ion homeostasis and blood flow. Cultivation dramatically changes the gene expression. In contrast, mild hypoxia showed only small changes. The changes are interpreted as stress response. We used this analysis as screening approach to detect significant changes in gene expression and used the RT-PCR analyses of independent sister cultures for confirmation. Correlation analysis showed close relations of the expression levels when aliquots of the biological material were compared. However, comparisons of the expression levels received by microarray and by RT-PCR analysis of independent sister samples resulted in 70-90 % in similar predictions. This data indicate that possible discrepancies has its basis in biological sampling rather than factors of methodical errors on the level of RT-PCR. Experiment Overall Design: Pooled samples of the following cochlea preparations were studied: Experiment Overall Design: (i) Native preparations of Organ of Corti, modiolus and stria vascularis from newborn rats used as controls; (ii) Organotypic cultures of these preparations under normoxic conditions (24 h); (iii) Cultures which were exposed to 5 h hypoxia during cultivation. Samples were collected for total RNA immediately after preparation of the inner ear structures (native samples) or 24 h after onset of cultivation (normoxia, hypoxia).
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Expression of apoptosis-related genes in the organ of Corti, modiolus and stria vascularis of newborn rats. Johann Gross, Astrid Machulik, Nyamaa Amarjargal, Renate Moller, Ute Ungethüm, Ralf-Jürgen Kuban, Frank-Uwe Fuchs, Nadezhda Andreeva, Julia Fuchs, Wolfgang Henke, Elena E Pohl, Agnieszka J Szczepek, Heidemarie Haupt, Birgit Mazurek. Brain Res 1162:56-68 (2007)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-5446.idf.txt
Sample and data relationshipE-GEOD-5446.sdrf.txt
Raw data (1)E-GEOD-5446.raw.1.zip
Processed data (1)E-GEOD-5446.processed.1.zip
Array designA-AFFY-22.adf.txt
R ExpressionSetE-GEOD-5446.eSet.r
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