| Experiment Id | GSE206673 | Name | Transcriptome dynamics in developing larynx, trachea, and esophagus |
| Experiment Type | RNA-Seq | Study Type | Baseline |
| Source | GEO | Curation Date | 2023-03-14 |
| description | The larynx, trachea, and esophagus share origin and proximity during embryonic development, with clinical and experimental evidence supporting the existence of neurophysiological, structural, and functional interdependencies before birth. This investigation provides the first comprehensive transcriptional profiling of all three organs during embryonic organogenesis, where differential gene expression gradually assembles the identity and complexity of these proximal organs from a shared origin in the anterior foregut. Through the application of bulk RNA sequencing and gene network analysis of differentially expressed genes (DEGs), both within and across developing embryonic mouse larynx, esophagus, and trachea, we identified co-expressed modules of genes enriched for key biological processes. Organ-specific temporal patterns of gene activity corresponding to gene modules within and across shared tissues during embryonic development (E10.5-E18.5) are described, and the laryngeal transcriptome during vocal fold development and maturation from birth to adult is characterized in the context of laryngeal organogenesis. The findings of this study provide new insights into interrelated gene sets governing organogenesis of this tripartite organ system within the aerodigestive tract, with relevance to multiple families of disorders defined by cardiocraniofacial syndromes. Wild type FVB/N mice males and females were mated, when vaginal plugs were found noon of that day was designated as embryonic day (E) 0.5. For RNA-Seq, pregnant females were sacrificed at E10.5, E11.5, E13.5, E15.5, E18.5, mouse larynges, trachea and esophagus were dissected, tissues were pooled together from 10 animals at E10.5, E11.5, E13.5, E18.5 time points, and 20 animals at the E15.5 timepoint. Approximately ~1-3 mm pieces of tissue were excised separately from the LPh/larynx (E10.5-Adult), esophagus (E10.5-E18.5) dorsoposterior to the larynx, and trachea (E10.5-E18.5) ventroposterior to the larynx with two medial biological replicates used at each timepoint. Tissue was collected anteriorly at the level of the LPh (E10.5 and E11.5) and vocal folds (E13.5 to adult) for the larynx and immediately posterior to the larynx in the case of both the esophagus and trachea. Additional timepoints for postnatal stage 0 (P0) and adult (6-8 weeks) larynx were included in the "within tissue" laryngeal analysis, where bulk tissue was collected at the level of the bilateral vocal folds. All tissues were micro-dissected in an RNase-free environment and immersed in RNAlater (Qiagen, Valencia, CA) at 4°C overnight, and then transferred to 80°C for long term storage prior to RNA extraction. |
