RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants transcriptome
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. Overall design: Axolotl embryos were obtained from the Ambystoma Genetic Stock Center at the University of Kentucky and incubated in 20% Holtfreter's solution at 22°C. Oropharyngeal endodermal explants were isolated at stage 15. Explants were harvested at stages 37/38, 39 and 41.  Replicate samples for each stage were analyzed for RNA quantity and quality on a Nanodrop 8000 spectrophotometer. Single-end read RNAseq of RNA isolated from axolotl embryonic oropharyngeal endoderm explants. High-throughput sequencing performed with Illumina NextSeq 500 System. Please note that the gene isoform counts were collapsed to gene counts for quantification across the samples (as in the 'Trinity.fasta.gene_trans_map')