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Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants.

ABSTRACT: Animal nutrition and toxin deterrence rely on the ability to taste, which occurs through columnar taste cells clustered within taste buds. Taste buds in mammals are located within specialized tissues, called papillae. However, taste buds in fish and amphibians, such as axolotls (Ambystoma mexicanum), are not housed in papillae, rather they are embedded 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. 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 a de novo assembly of the transcriptome using a Trinity pipeline. From 27.9Gb of raw sequences, we identified 21,244 transcripts. To our knowledge, this is the first published assembly of axolotl oropharyngeal endoderm explants. This data and transcriptome assembly relate to the research article "Transcriptome Analysis of Axolotl Oropharyngeal Explants During Taste Bud Differentiation Stages" (Kohli et al. 2020). 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.

SUBMITTER: Marazzi L

PROVIDER: S-EPMC7419325 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundTraumatic spinal cord injury (SCI) is a disabling condition that affects millions of people around the world. Currently, no clinical treatment can restore spinal cord function. Comparison of molecular responses in regenerating to non-regenerating vertebrates can shed light on neural restoration. The axolotl (Ambystoma mexicanum) is an amphibian that regenerates regions of the brain or spinal cord after damage.MethodsIn this study, we compared the transcriptomes after SCI at acute (1-2 days after SCI) and sub-acute (6-7 days post-SCI) periods through the analysis of RNA-seq public datasets from axolotl and non-regenerating rodents.ResultsGenes related to wound healing and immune responses were upregulated in axolotls, rats, and mice after SCI; however, the immune-related processes were more prevalent in rodents. In the acute phase of SCI in the axolotl, the molecular pathways and genes associated with early development were upregulated, while processes related to neuronal function were downregulated. Importantly, the downregulation of processes related to sensorial and motor functions was observed only in rodents. This analysis also revealed that genes related to pluripotency, cytoskeleton rearrangement, and transposable elements (e.g., Sox2, Krt5, and LOC100130764) were among the most upregulated in the axolotl. Finally, gene regulatory networks in axolotls revealed the early activation of genes related to neurogenesis, including Atf3/4 and Foxa2.ConclusionsImmune-related processes are upregulated shortly after SCI in axolotls and rodents; however, a strong immune response is more noticeable in rodents. Genes related to early development and neurogenesis are upregulated beginning in the acute stage of SCI in axolotls, while the loss of motor and sensory functions is detected only in rodents during the sub-acute period of SCI. The approach employed in this study might be useful for designing and establishing regenerative therapies after SCI in mammals, including humans.

Dataset Information

Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants.

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