Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Scott Pletcher

PROVIDER: E-GEOD-16744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.

Montemayor Celina C Montemayor Oscar A OA Ridgeway Alex A Lin Feng F Wheeler David A DA Pletcher Scott D SD Pereira Fred A FA

PloS one 20100127 1

<h4>Background</h4>Identification of bona fide direct nuclear receptor gene targets has been challenging but essential for understanding regulation of organismal physiological processes.<h4>Results</h4>We describe a methodology to identify transcription factor binding sites and target genes in vivo by intersecting microarray data, computational binding site queries, and evolutionary conservation. We provide detailed experimental validation of each step and, as a proof of principle, utilize the m ...[more]

PMID: 20111703

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Dataset Information

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

Publications

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.

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