Mus musculus
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-16744
PROVIDER: PRJNA117441 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to establish a list of candidate direct COUP-TFI gene targets in the inner ear, we analyzed the differential gene expression profiles of the wild-type and the COUP-TFI–/– P0 inner ears.
2010-05-31 | GSE16744 | GEO
Project description:In order to establish a list of candidate direct COUP-TFI gene targets in the inner ear, we analyzed the differential gene expression profiles of the wild-type and the COUP-TFIâ/â P0 inner ears. We performed a total of 8 microarray experiments using Affymetrix MG-U74Av2 chips, including 2 biological and 2 experimental replicates per genotype sample. Due to limiting RNA yields from the newborn inner ear, each microarray chip was hybridized with an RNA pool from multiple tissue samples. We analyzed our data using two different algorithms: GC-Robust Multi-Array (GCRMA) and dChip. Each normalized expression dataset was subsequently analyzed by 2-way ANOVA, evaluating both genotype and experimental effects. This statistical approach allowed us to 1) account for an experimental effect observed in the expression value of many genes, therefore increasing the power of the analysis, and 2) filter out potential expression differences due to contamination during dissections (contaminating genes would present as probes with a significant interaction p-value). Using this methodology, the gene hits from the GCRMA-normalized expression dataset consisted of 256 genes with a significant genotype effect (p<0.01) and no interaction (p>0.01). Similar cutoffs applied on the dChip-normalized dataset resulted in 250 significant gene hits. Within both groups, COUP-TFI has the lowest genotype p-value, validating our statistical approach.
2010-06-08 | E-GEOD-16744 | biostudies-arrayexpress
Project description:Transcription profiling by array of mouse newborn inner ears from wild type and COUP-TFI -/- mice
2014-07-09 | E-GEOD-16744 | ExpressionAtlas
Project description:The genome-wide binding sites of COUP-TFI in neural retina.
2023-12-31 | GSE190657 | GEO
Project description:Purpose: The goal of this study is to compare the expression profile of wild type and Tbx1-nmf219/nmf219 mice with NGS-derived inner ear transcriptome profiling (RNA-seq) Methods: inner ear mRNA profiles of E16.5 wild-type (WT) and Tbx1-nmf219/nmf219mice were generated by RNA-seq Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome and identified transcripts in the inner ear of WT and Tbx1nmf219/nmf219 mice. Approximately 10% of the transcripts showed differential expression between the WT and Tbx1nmf219/nmf219 inner ear, with a fold change ≥1.5 and p value <0.05. Conclusions: Our study represents the detailed analysis of inner ear transcriptomes, with biologic replicates, generated by RNA-seq technology.
2019-10-01 | GSE134756 | GEO
Project description:These data support a translational control of COUP-TFI gradient expression by FGF8 via miR-21 and contribute to our understanding of how regionalized expression is established during neocortical area mapping
2018-08-01 | GSE117932 | GEO
Project description:MicroRNAs (miRNAs) inhibit the translation of target mRNAs and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. This study focuses on miRNAs that are expressed in the mouse cochlea and vestibule, the two inner ear compartments. To identify miRNAs that are expressed in the vertebrate developing inner ear, we used miRNA microarrays. Similar miRNA profiles were found in newborn (P0) mouse whole cochleae and vestibules. 105 miRNAs were found to be expressed in the whole P0 cochlea and 114 miRNAs expressed in the whole P0 vestibule with average intensities higher than twice the global background, out of 206 included in the arrays. Only 24 miRNAs were found to have different levels of expression in these whole organs, and these differences were mild (15-40%). The microarray results were intersected with two bioinformatic complementary approaches in order to choose candidate miRNAs that are predicted to be expressed specifically in the inner ear sensory epithelia (see the paper).
2009-04-02 | GSE15496 | GEO
Project description:In this study, we generated a human inner ear atlas containing three stages of inner ear development. This atlas was used to evaluate the differentiation approach of human pluripotent stem cells in to complex inner ear tissue, known as inner ear organoids. The primary goal of this single-nucleus RNA-sequencing analysis was to capture the cell type diversity of the human inner ear at different stages of development. The secondary goal was to define the similarity of organoid-derived inner ear cell types with the atlas-derived human inner ear cell types and to determine the developmental stage of the organoid-derived inner ear cell types.
2023-06-05 | GSE213796 | GEO