Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparison of organ of Corti RNA from Ptprq-CAT-KO homozygotes and wildtype littermates

ABSTRACT: Ptprq is one of the genes markedly downregulated in the diminuendo mouse, which carries a mutation in the microRNA miR-96. We carried out microarrays on mice homozygous for a functional null allele of Ptprq and their wildtype littermates to compare expression changes to those seen in diminuendo homozygotes and examine how much, if any, of the diminuendo transcriptional phenotype can be explained by the downregulation of Ptprq.

ORGANISM(S): Mus musculus

SUBMITTER: Morag Lewis

PROVIDER: E-MTAB-1785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A reduction in Ptprq associated with specific features of the deafness phenotype of the miR-96 mutant mouse diminuendo.

Chen Jing J Johnson Stuart L SL Lewis Morag A MA Hilton Jennifer M JM Huma Andreea A Marcotti Walter W Steel Karen P KP

The European journal of neuroscience 20140122 5

miR-96 is a microRNA, a non-coding RNA gene which regulates a wide array of downstream genes. The miR-96 mouse mutant diminuendo exhibits deafness and arrested hair cell functional and morphological differentiation. We have previously shown that several genes are markedly downregulated in the diminuendo organ of Corti; one of these is Ptprq, a gene known to be important for maturation and maintenance of hair cells. In order to study the contribution that downregulation of Ptprq makes to the dimi ...[more]

PMID: 24446963

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Project 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 shortâterm 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).

Dataset Information

Comparison of organ of Corti RNA from Ptprq-CAT-KO homozygotes and wildtype littermates

Publications

A reduction in Ptprq associated with specific features of the deafness phenotype of the miR-96 mutant mouse diminuendo.

Similar Datasets

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