Single cell transcriptome analysis of developing arcuate nucleus neurons uncovers their key developmental regulators

This report contains a scRNA-seq analysis of E15 hypothalamic arcuate nucleus (ARC), which uncovers many cell type-specific markers, including a group of transcription factors. This study newly demonstrate critical roles of two of these transcription factors in specifying the identity of ARC neurons. Many of these transcription factors are enriched in specific single cell transcriptomes while being excluded from other single cell transcriptomes, suggesting their crucial roles in cell fate determination. A single sample was sequenced multiple times to increase coverage. Single cell RNA-seq data were generated on the 10X emulsion platform (10X Genomics, Pleasanton, CA) according to the manufactures instructions. The single-cell RNAseq from the Chromium platform was processed using CellRanger v2.1.1, and subsequent normalization, QC, filtering, differential gene expression analysis, and dimension reduction was performed in R using Seurat v2.0 (http://www.satijalab.org/seurat).本报告针对胚胎第15天（E15）的下丘脑弓状核（hypothalamic arcuate nucleus, ARC）开展了单细胞RNA测序（single cell RNA-seq, scRNA-seq）分析，揭示了多种细胞类型特异性标志物，其中涵盖一组转录因子。本研究新近证实，其中两种转录因子在调控ARC神经元身份特化过程中发挥关键作用。此类转录因子中，多数在特定单细胞转录组中呈富集表达状态，而在其余单细胞转录组中表达被抑制，这提示它们在细胞命运决定过程中具有不可或缺的重要功能。为提升测序覆盖深度，本研究对单个样本进行了多次测序。本研究依托10X微乳液平台（10X Genomics，美国加利福尼亚州普莱森顿），严格遵循制造商操作手册完成单细胞RNA测序实验。基于Chromium平台获得的单细胞RNA测序数据，采用CellRanger v2.1.1进行预处理；后续的标准化、质量控制、过滤、差异基因表达分析及降维操作，均通过R语言环境下的Seurat v2.0工具包（http://www.satijalab.org/seurat）完成。