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Mus musculus

ABSTRACT: Wild-type and COUP-TFI-/- newborn inner ear microarrays

OTHER RELATED OMICS DATASETS IN: E-GEOD-16744

PROVIDER: PRJNA117441 | ENA |

REPOSITORIES: ENA

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Wild-type and COUP-TFI-/- newborn inner ear microarrays

2010-05-31 | GSE16744 | GEO

Wild-type and COUP-TFI-/- newborn inner ear microarrays

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

E-GEOD-16744

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

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ChIP-seq analysis of COUP-TFI enrichment in neural retina.

Project description:The genome-wide binding sites of COUP-TFI in neural retina.

2023-12-31 | GSE190657 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tbx1-nmf219/nmf219 inner ear Transcriptomes

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.

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The microRNA miR-21 is a mediator of FGF8 action on cortical COUP-TFI translation

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

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