Non-visual photoreceptive brain specification in sea urchin larvae

We employed the Western Pacific model sea urchin, Hemicentrotus pulcherrimus, as our experimental system to establish a comprehensive single-cell RNA sequencing (scRNA-seq) data atlas. Our primary objective was to document stage-specific gene expression profiles during the normal developmental progression, ranging from 24 to 96 hours post-fertilization. Our particular focus lay on neurogenesis, a pivotal process occurring in the latter stages of sea urchin development. To elucidate the regulatory mechanisms governing neurogenesis, we utilized pharmacological interventions targeting the Delta-Notch signaling pathway, a central regulator of this process. By perturbing the pathway's lateral inhibition from 16 hours post-fertilization, we aimed to identify gene sets typically suppressed during neurogenesis. Subsequent to the inhibition, we observed a notable upregulation of neurogenic genes and a concurrent expansion in the cellular population expressing these genes, starting from the 24-hour time point. In addition, the processed Seurat objects (RDS files), stratified by developmental stage, experimental condition, and sample, are available through the HpHase portal (https://cell-innovation.nig.ac.jp/Hpul/). Overall design: To construct a comprehensive single-cell RNA sequencing (scRNA-seq) atlas of sea urchin development, we acquired datasets from embryos/larvae at 24, 36, 48, 72, and 96-hour time points utilizing the 10xChromium methodology. Additionally, to enhance the resolution of neuronal gene expression patterns, we employed DAPT to inhibit lateral inhibition, thereby promoting neural fate determination during sea urchin development. Subsequently, scRNA-seq data were gathered from the DAPT-treated cohort.