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. Overall design: 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).