Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of mouse olfactory sensory neurons expressing 3 different types of olfactory receptor

ABSTRACT: The goal of RNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR. The GFP knockin mice (Olfr73-IRES-GFP, Olfr1507-IRES-GFP, and Olfr160-IRES-mCherry) was used to label the OSN expressing specific OR. These cells was then isolate with fluorescence activated cell sorting. For each sample, at least 5000 cells are collected, there biological replicates were collected for each genotype and in total 9 samples were prepared for RNA-seq libraries with using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair. Libraries were sequenced using paired end 150 cycle reads on an Illumina Hiseq4000 (Novogene). The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively. Differential analysis were conducted in DESeq2. The significant genes were deducted by computing Wald test with corrected p < 0.05. Our results shows that different types of OSNs express significantly different patterns of genes, especially the genes involved in axonal guidance.

ORGANISM(S): Mus musculus

PROVIDER: GSE169010 | GEO | 2022/01/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-cell transcriptome analysis of mouse main olfactory epithelium

Project description:The goal of scRNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR in a large and unbias scale. Olfactory epithelial single cell suspensions were made using 3 male and 3 female mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene). The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=420, default settings except STAR v2.6.1 was used for alignment).

2022-01-31 | GSE169011 | GEO

Transcription profiling of mouse olfactory sensory neurons

Project description:The overall aim of the experiment is to understand the phenotype of mature mouse olfactory sensory neurons by analyzing the transcripts expressed and enriched in them as compared to the rest of the cell types in the olfactory epithelium (consisting of immature neurons, supporting cells, progenitor cells and cells in lamina propria) and brain ( with out the olfactory bulbs). Comparision with the other cell types in the olfactory epithelium should eliminate the transcripts commonly expressed in the olfactory epithelium and comparision with brain will eliminate the transcripts common to most neurons. Our gene chip data indicates that mature mouse olfactory sensory neurons express 10,000 genes. Mature OSNs specifically contained three clusters of over represented Gene ontology categories: smell, ion transport and cilia. Analysis for the functionally over represented categories among the transcripts with a positive signal in the mature OSNs yielded largely broad categories common to all cells with the exception of chromatin modelling and RNA processing categories. Biological process categories of movement, development and immune response came as under represented categories. Experiment Overall Design: To purify mature olfactory neurons we took advantage of the OMP-GFP mice. OMP(olfactory marker protein) is expressed specifically in mature olfactory and vomeronasal sensory neurons. In the OMP-GFP mice the coding region of OMP is replaced by GFP. We purified OSNs from the rest of the epithelium from these mice by using FACS. . We used the Affymetrix gene chips mouse expression set 430 (consisting of 430A and 430B chips). Our gene chip data is extensively validated by insitu hybridizations.

2008-06-13 | E-GEOD-4915 | biostudies-arrayexpress

Single-cell RNA-sequencing of OMP-GFP mouse olfactory sensory neurons

Project description:We sequenced the transcriptome of 34 single olfactory sensory neurons (OSNs) manually picked from OMP-GFP mice, ensuring the cells expressed high levels of GFP, a marker of mature OSNs. We pooled the olfactory mucosa from 2 male and 2 female animals, to obtain single-cell suspensions for cell picking. We only picked healthy-looking cells. From each, we constructed libraries for single-cell RNA-sequencing, to characterise the diversity of OR genes expressed.

2020-02-04 | E-MTAB-8285 | biostudies-arrayexpress

Effects of olfactory-specific Bcl11b overexpression on gene expression in the main olfactory epithelium of neonatal mice.

Project description:Individual olfactory sensory neurons (OSNs) express a single odorant receptor (OR) gene from the class I or class II repertoire in mice. The mechanisms that regulate the binary fate specification of OSNs remain unknown. Here we show that the transcription factor Bcl11b, which is expressed in class II OSNs determines the OR class to be expressed in OSNs. Genetic studies provide evidence that class I is a default-fate and Bcl11b permits a class II fate by suppressing a class I-OR enhancer. These findings reveal a unique transcriptional mechanism that serves as a binary switch to select the OR class and is crucial to both the anatomical and functional organization of olfactory system.

2019-08-07 | GSE118169 | GEO

Comparison of olfactory sensory neuron subtypes

Project description:Olfactory sensory neurons (OSNs) express a single abundant olfactory receptor (OR). To assess the differences in gene expression between different OSN sub-types we collected three pools of neurons that express one OR and compared them to three pools of neurons that express another. After extracting RNA from these pools, the samples were multiplexed and sequenced using the Illumina Hiseq2500 platform.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-02-09 | E-ERAD-436 | biostudies-arrayexpress

Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons

Project description:Olfaction plays important roles in food and mate choice, and also in the avoidance of predators, making it a vital sensory modality for preservation and reproduction. In the vertebrates, olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons (OSNs). Although olfactory cilia dysfunction can cause loss of the sense of smell, how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1, a fork head-domain containing transcription factor traditionally linked with motile cilia biogenesis, is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia, we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells, are repressed in the OSNs. Strikingly, we also found that besides ciliogenesis, Foxj1 controls the differentiation of the OSNs by regulating their cell type-specific gene expression, such as that of olfactory marker protein (omp) involved in odour-evoked signal transduction. In line with these requirements, response to bile acid, an odour detected by OMP-positive OSNs, was significantly diminished in the foxj1 mutant zebrafish. Taken together, our findings establish how the canonical Foxj1-mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves.

2023-12-04 | GSE232397 | GEO

Transcription profiling of mouse olfactory epithelium from heterozygous and homozygouse OMP-GFP animals

Project description:OMP is expressed only in mature olfactory sensory neurons, arguing that its function is specially suited to the needs of OSNs. However none of the properties of OMP suggest any direct role in regulating gene expression in OSNs. Our data confirms that gene expression in the olfactory epithelium of mice lacking OMP is indistinguishable from mice expressing OMP. We used affymerix M430v2.0 gene chips to cover as much of genome as possible and observed no statistically significant differences in mRNA abundance between the two genotypes.These results imply that OMPs ability to regulate signal transduction with in OSNs has little effect on gene expression and that its ability to promote mitosis in neighbouring cells (under culture conditions) is insufficiently active under normal laboratory housing conditions to generate detectable differences in gene expression patterns. Experiment Overall Design: The overall design of the experiment is to undertand the effect of OMP (olfactory marker protein) on gene expression in the olfactory epithelium. We isolated the olfactory epithelium from homozygous and heterozygous OMP-GFP mice, extracted the RNA and hybridized on to the mouse expression set 430 2.0 Chip.

2008-06-13 | E-GEOD-4927 | biostudies-arrayexpress

Transcripts enriched in mouse olfactory sensory neurons

2007-04-30 | GSE4915 | GEO

Coordination of two enhancers drives expression of olfactory trace amine-associated receptors VII

Project description:Olfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.

2021-03-08 | GSE163776 | GEO

Coordination of two enhancers drives expression of olfactory trace amine-associated receptors III

2021-03-08 | GSE163671 | GEO