The inner ear comprises four epithelial domains: the cochlea, vestibule, semicircular canals, and endolymphatic duct/sac. These structures are segregated at embryonic day 13.5 (E13.5). However, these four anatomical structures remain undefined at E10.5. Here, we aimed to identify lineage-specific genes in the early developing inner ear using published data obtained from single-cell RNA-sequencing (scRNA-seq) of embryonic mice. We downloaded 5000 single-cell transcriptome data, named ‘auditory epithelial trajectory’, from the Mouse Organogenesis Cell Atlas. The dataset was supposed to include otic epithelial cells at E9.5–13.5. We projected the 5000 ​cells onto a two-dimensional space encoding the transcriptional state and visualised the pattern of otic epithelial cell differentiation. We identified 15 clusters, which were annotated as one of the four components of the inner ear epithelium using known genes that characterise the four different tissues. Additionally, we classified 15 clusters into sub-regions of the four inner ear components. By comparing transcriptomes between these 15 clusters, we identified several candidates of lineage-specific genes. Characterising these new candidate genes will help future studies about inner ear development.

内耳包含四个上皮区域：耳蜗，前庭，半圆形管和内淋巴管/囊。这些结构在胚胎第13.5天（E13.5）分离。但是，这四个解剖结构在E10.5上仍未定义。在这里，我们旨在使用从胚胎小鼠单细胞RNA测序（scRNA-seq）获得的公开数据，在发育中的内耳中鉴定谱系特异性基因。我们从小鼠器官发生细胞图谱下载了5000个单细胞转录组数据，称为“听觉上皮轨迹”。该数据集被认为包括E9.5-13.5的耳上皮细胞。我们将5000个细胞投影到编码转录状态的二维空间上，并观察耳上皮细胞分化的模式。我们确定了15个集群 使用已知的表征四种不同组织的基因，将其标记为内耳上皮的四个成分之一。此外，我们将15个簇分类为四个内耳组件的子区域。通过比较这15个簇之间的转录组，我们确定了几种谱系特异性基因的候选基因。表征这些新的候选基因将有助于未来有关内耳发育的研究。