Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB20276 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR641559.fastq.gz | Fastqsanger.gz | |||
| DRR641560.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Comprehensive single-cell RNA transcriptomic analysis of hypopharyngeal epithelium of mice
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Project description:In this study, we uncovered through single cell RNA sequencing (scRNA-seq) of mouse esophagus epithelium a population of taste buds clustered in the cervical segment of the esophagus. We compared this taste bud population to their lingual counterpart. We concluded that these taste buds have the same cellular composition than the ones from the tongue. State-of-the-art transcriptional regulatory network analysis allowed the identification of specific transcription factors associated to the differentiation of immature progenitors into the three different taste bud cell types in the tongue and the esophagus.
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Project description:Taste buds are complex sensory organs that are embedded in the epithelium of fungiform papillae (FP) and circumvallate papillae (CV). The sweet, bitter, and umami taste are sensed by type II taste cells that expressed taste receptors (Tas1rs and Tas2rs) which coupled with taste G-protein α-gustducin. Recent studies revealed that the taste response profiles of α-gustducin-expressing cells are different between FP and CV. We applied the high-throughput single-cell RNA-sequencing combined with fluorescence-activated cell sorting (FACS) to profile the transcriptome of the α-gustducin-expressing taste cells in both fungiform and circumvallatae papillae with transgenic mice expressing green fluorescent protein (GFP).
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Project description:The ability to taste is critical for animal nutrition and toxin deterrence. The majority of research on taste bud development and regeneration is in mice, where taste buds are located within specialized papillae on the tongue. However, taste buds in fish and amphibians, such as axolotls (Ambystoma mexicanum), are not housed in papillae, rather they are within the pharyngeal epithelium. This simplified tissue level organization, along with the ability of cultured oropharyngeal explants from early embryos to produce taste buds on the same time-line as embryos, make the axolotl an excellent model to identify molecules specifically involved in taste bud cell differentiation. In this study, we performed de novo transcriptomic analysis on RNA sequences from three different stages of oropharyngeal explants: stages 37/38, 39, and 41. RNA-seq data from 17 total samples representing these stages were pooled to generate de novo assemblie(s) of the transcriptome using a Trinity pipeline. Raw reads and the assembly were uploaded to Mendeley (doi:10.17632/tvxh3jm83m.1). From 27.9Gb of raw sequences, we identified 21,244 transcripts. To our knowledge, this study provides the first published assembly of axolotl oropharyngeal endoderm explants. This RNA-seq data and transcriptome assembly provide information on genes expressed in the oropharyngeal endoderm and will be valuable in the identification of taste bud development genes.
2020-06-02 | GSE151535 | GEO
Project description:We have recently demonstrated that Sox10-expressing (Sox10+) cells give rise to mainly type-III neuronal taste bud cells that are responsible for sour and salt taste. The two tissue compartments containing Sox10+ cells in the surrounding of taste buds include the connective tissue core of taste papillae and von Ebner’s glands (vEGs) that are connected to the trench of circumvallate and foliate papillae. Here we present data to support that it is the vEGs, not connective tissue core, that serve as the niche of Sox10+ taste bud progenitors. In this study, we performed single cell RNA-sequencing of the epithelium of Sox10-Cre/tdT mouse circumvallate/vEG complex and used inducible Cre mouse models to map the cell lineages of vEGs and/or connective tissue (including stromal and Schwann cells). Transcriptomic analysis indicated that Sox10 expression was enriched in the cell clusters of vEG ducts that contained abundant proliferating cells, while Sox10-Cre/tdT expression was enriched in type-III taste bud cells and vEG ductal cells. In vivo lineage mapping showed that the traced cells were distributed in circumvallate taste buds concurrently with those in the vEGs, but not in the connective tissue. Moreover, multiple genes encoding pathogen receptors were enriched in the vEG ducts hosting Sox10+ cells. If this is also true in humans, our data indicates that vEG duct is a source of Sox10+ taste bud progenitors and susceptible to pathogen infections.
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Project description:Comprehensive single-cell transcriptomic analysis of laryngeal epithelium of mice
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Project description:Purpose: The goal of this study is to compare the taste bud transcriptome of fasted and fed mice. By doing this we hope to gain more information about the taste bud transcriptome as well as determine transcriptional changes that may be linked with pre or post-ingestive states. Methods: Whole taste bud mRNA profiles of WT adult C57BL/6J mice were generated by Illumina HiSeq 2000 single end RNA sequencing. Prior to taste bud RNA isolation, mice were either food-deprived, fed, or given ad libitum access to standard rodent chow as a control. Sequence read quality was assesed using FastQC, and adapter sequences were trimmed using trimmomatic. Reads were then aligned to the GRCm38.p4 reference genome using Tophat2 followed by Cufflinks analysis, then gene level differential expression was conducted using Cuffdiff, and visualized via cummeRbund. Gene enrichment analysis of differentially expressed genes was performed using DAVID and Panther Gene Ontology. Results: We mapped about 30 million sequence reads per sample to the mouse genome, build GRCm38.p4, and identified 144 differentially expressed genes (FDR of 5%) between the taste buds of food-restricted, fed, and ad libitum control mice. Gene enrichment analysis of differentially expressed genes showed enrichment of pathways associated with cytokines, immunity, cytoskeletal structure, chaperone proteins, and protease inhibitors. Conclusions: Our study represents a detailed analysis of the murine taste bud transcriptome generated using RNA-seq technology. Our results highlight cellular pathways that may be differentially regulated in taste receptor cells during different pre/post-ingestive states. Additionally, as limited transcriptome information is available for taste buds, this dataset can serve as a resource for the discovery of genes novel to the taste bud.
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