Mus musculus
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ABSTRACT:
PROVIDER: PRJNA139871 | ENA |
REPOSITORIES: ENA
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Project description:Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets. Beta3GnT1 mutant mice lose lactosamine expression and have an olfactory axon guidance phenotype (Henion et al, 2005). Olfactory neurons are capable of regeneration and we know that when these neurons regenerate in beta3GnT1 mutant they synthesize lactosamine by a secondary mechanism. By comparing RNA from the olfactory epithelium from wild type and mutant mice, we would expect to see the upregulation of glycosyltransferases that could produce lactosamine in the absence of beta3GnT1. In a preliminary experiment carried out by the CFG staff, we saw that radical fringe, a beta 3GnT, was upregulated in the olfactory epithelium, although it is probably not responsible for the new lactosamine expression. beta3GnT1 Knock out. Strain info: The b3GnT1 mice were generated on a mixed 129Ola-C57BL/6 background and backcrossed to C57BL/6 for four generations. They were then crossed to I7-Internal ribosomal entry site (IRES)-tau greeen fluorescent protein (GFP) mice generated by Dr. Peter Mombaerts. RNA preparations from wild type and beta3GnT1 mutant mouse olfactory epithelium were sent to Microarray Core (E). Three replicate samples from each condition were used in the study. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to determine glycosyltransferase expression changes in beta3GnT1 mutant mice, with specific interest on glycosyltransferases that could produce lactosamine in the in the absence of beta3GnT1.
2011-04-29 | E-GEOD-28926 | biostudies-arrayexpress
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Project description:Sham and bilateral OBX were performed on wild-type and SR-A mutant mice. Tissue collected 2, 8, 16, and 48 hours following OBX. Expression profiles were determined using Affynetrix MG U74Av2 chips. Experiment Overall Design: olfactory epithelium from 3 wild type 6 week old mice and 3 SR-A 6 week old mutant mice
2007-11-22 | E-GEOD-3455 | biostudies-arrayexpress
Project description:To quantify gene expression differences in olfactory epithelium between the mouse (Mus musculus) and the Nile rat (Arvicanthis niloticus), paired-end RNA sequencing (RNA-seq) was used to profile olfactory epithelium transcriptomes of six Nile rats and six mice (C57BL/6J) (one male and one female at the age of 8, 12, and 16 weeks for each species).
2022-05-01 | GSE201761 | GEO
Project description:Microarray analysis of gene expression in the olfactory epithelium of Harlequin mouse as a model of oxidative-stress induced neurodegeneration of olfactory sensory neurons Experiment Overall Design: Olfactory epithelium from Harlequin mutant mice and littermate control mice was microdissected for RNA extraction and hybridization on Affymetrix microarrays. We compared levels of gene expression in 6-month old mice to begin to identify mechanisms of oxidative-stress induced neurodegeneration and to correlate the cellular changes that we observed in the olfactory epithelium by using histology and immunohistochemistry with gene expression changes.
2008-06-14 | E-GEOD-6485 | biostudies-arrayexpress
Project description:RNAseq differential gene expression profiling of olfactory mucosa in young wild type, aged wild type, APP deficient, APLP2 deficient and PSEN2 deficient mice. Purpose: Next-generation gene expression profiling has revolutionized analysis of molecular pathways. The goals of this study were to compare NGS-derived olfactory mucosa transcriptome profiles (RNAseq) of aged wild-type mice, APP knockout mice, APLP2 knockout mice and PSEN2 knockout mice with young wild-type controls. Selected genes and pathways will be analyze further by low-throughput techniques such as real-time RT-PCR. Methods: Olfactory mucosa mRNA profiles of 2 months old wild-type (WT), 2 years old wild-type, APP knockout, APLP2 knockout and PSEN2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 . For inspecting the quality of RNA-Seq data, the 100 most abundant genes are taken from all the samples and heatmaps were generated to observe the relation between samples/conditions. The sequence reads that passed the quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using our data analysis workflow, we mapped at least 30 million sequence reads per sample to the mouse genome (build mm10) and identified approximately 25,867 transcripts in the olfactory epithelium of WT and genetically modified mice with TopHat workflow. RNAseq data confirmed stable expression of 20 known housekeeping genes, and 3 of them were validated with qRT-PCR. Approximately 20% of transcripts showed differential expression between WT and aged samples and 0.1-1.0 % showed differential expression between WT and genetically modified lines (fold change >1.5; p value < 0.05). Altered expression of 20 genes for aged samples and 10 genes for PS-deficient samples was confirmed by qRT-PCR, demonstrating the high degree of sensitivity of RNAseq approach. Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa in aged animals. It is also the first study examining effects of gene knockout for APP, APLP2 and PSEN2 on gene expression profile in murine olfactory mucosa. We conclude that these data would help future studies in olfactory mucosa cells aimed to reveal molecular mechanisms associated with aging and biological function of APP, APLP2 and PSEN2 genes. RNAseq differential gene expression profiling of olfactory mucosa in young wild type, aged wild type, APP deficient, APLP2 deficient and PSEN2 deficient mice. Purpose: Next-generation gene expression profiling has revolutionized analysis of molecular pathways. The goals of this study were to compare NGS-derived olfactory mucosa transcriptome profiles (RNAseq) of aged wild-type mice, APP knockout mice, APLP2 knockout mice and PSEN2 knockout mice with young wild-type controls. Selected genes and pathways will be analyze further by low-throughput techniques such as real-time RT-PCR. Methods: Olfactory mucosa mRNA profiles of 2 months old wild-type (WT), 2 years old wild-type, APP knockout, APLP2 knockout and PSEN2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 . For inspecting the quality of RNA-Seq data, the 100 most abundant genes are taken from all the samples and heatmaps were generated to observe the relation between samples/conditions. The sequence reads that passed the quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using our data analysis workflow, we mapped at least 30 million sequence reads per sample to the mouse genome (build mm10) and identified approximately 24,000 transcripts in the olfactory epithelium of WT and genetically modified mice with TopHat workflow. RNAseq data confirmed stable expression of 20 known housekeeping genes, and 3 of them were validated with qRT-PCR. Approximately 20% of transcripts showed differential expression between WT and aged samples and 0.1-1.0 % showed differential expression between WT and genetically modified lines (fold change >1.5; p value < 0.05). Altered expression of 20 genes for aged samples and 10 genes for PS-deficient samples was confirmed by qRT-PCR, demonstrating the high degree of sensitivity of RNAseq approach. Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa in aged animals. It is also the first study examining effects of gene knockout for APP, APLP2 and PSEN2 on gene expression profile in murine olfactory mucosa. We conclude that these data would help future studies in olfactory mucosa cells aimed to reveal molecular mechanisms associated with aging and biological function of APP, APLP2 and PSEN2 genes. This RNAseq project has been supported by a grant of Polish National Science Centre (UMO-2013/09/NZ3/02359).
2020-03-31 | GSE147771 | GEO
Project description:Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets. Beta3GnT1 mutant mice lose lactosamine expression and have an olfactory axon guidance phenotype (Henion et al, 2005). Olfactory neurons are capable of regeneration and we know that when these neurons regenerate in beta3GnT1 mutant they synthesize lactosamine by a secondary mechanism. By comparing RNA from the olfactory epithelium from wild type and mutant mice, we would expect to see the upregulation of glycosyltransferases that could produce lactosamine in the absence of beta3GnT1. In a preliminary experiment carried out by the CFG staff, we saw that radical fringe, a beta 3GnT, was upregulated in the olfactory epithelium, although it is probably not responsible for the new lactosamine expression. beta3GnT1 Knock out. Strain info: The b3GnT1 mice were generated on a mixed 129Ola-C57BL/6 background and backcrossed to C57BL/6 for four generations. They were then crossed to I7-Internal ribosomal entry site (IRES)-tau greeen fluorescent protein (GFP) mice generated by Dr. Peter Mombaerts.
2011-04-29 | GSE28926 | GEO
Project description:Transcriptional profile of the main olfactory epithelium (MOE) and the vomeronasal organ (VNO) of male wild type mice
2013-12-23 | E-MTAB-2163 | biostudies-arrayexpress
Project description:Transcriptome analysis of RNA samples from mice olfactory epithelium Gene expression profiling in the olfactory epithelium was performed to obtain a better understanding of the processes mediating cell replacement.
2013-04-11 | GSE45931 | GEO
Project description:Gene level analysis of RNA samples from mice olfactory epithelium Gene expression profiling in the olfactory epithelium was performed to obtain a better understanding of the processes mediating activity dependent gene regulation
2014-04-21 | GSE49998 | GEO