Differential gene expression in murine olfactory epithelium: effect of loss of ACE2
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ABSTRACT:
PROVIDER: PRJNA836627 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19149591_1.fastq.gz | Fastqsanger.gz | |||
| SRR19149591_2.fastq.gz | Fastqsanger.gz | |||
| SRR19149592_1.fastq.gz | Fastqsanger.gz | |||
| SRR19149592_2.fastq.gz | Fastqsanger.gz | |||
| SRR19149593_1.fastq.gz | Fastqsanger.gz |
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Project description:RNAseq differential gene expression profiling of olfactory mucosa in young wild type, ACE2 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 wild-type mice (control) and ACE2 knockout mice. 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) and ACE2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 S4 PE150 XP. 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. Results: Using our data analysis workflow, we mapped at least 47 million sequence reads per sample to the mouse genome (build mm10). Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa. It is also the first study examining effects of gene knockout for ACE2 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 ACE2 genes. RNAseq differential gene expression profiling of olfactory mucosa in wild type and ACE2 deficient mice.
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Project description:Expression profiling of mRNA abundance in the adult mouse olfactory epithelium during replacement of OSNs forced by the bilateral ablation of the olfactory bulbs. The experiment was done on 6 week old male C57Bl/6 mice. Olfactory epithelium tissue samples were collected on days 1, 5, and 7 after bulbectomy. The cellular processes activated by bulbectomy include apoptosis of mature olfactory sensory neurons, infiltration of macrophages and dendritic cells, stimulation of proliferation of basal cell progenitors, and differentation of new sensory neurons.
2007-09-04 | E-GEOD-2437 | biostudies-arrayexpress
Project description:We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment. The objective of generating this dataset was to analyze the effects of H2be loss of function on gene expression in the main olfactory epithelium of 6-month old mice. This dataset compares gene expression in wild type and H2be-KO main olfactory epithelium (MOE) samples. There are six replicates for each genotype (equal mixture of males and females).
2012-09-01 | E-GEOD-39515 | biostudies-arrayexpress
Project description:Mouse Olfactory Epithelium, whole olfactory mucosa, mouse
| PRJNA660060 | ENA
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).
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Project description:Mouse olfactory sensory neurons, main olfactory epithelium and main olfactory bulb
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Project description:Differential gene expression in murine olfactory epithelium: effect of aging and loss of APP, APLP2 and PSEN2.
| PRJNA616336 | ENA