Droplet-based scRNA-seq of plasma-positive microglia and plasma-negative microglia from hypothalamus region in young mice

Microglia are highly responsive to their local environment and signals from the periphery. Blood plasma proteins readily permeate the healthy brain parenchyma. However, whether microglia are responsive to such proteins is unclear. Here, we identify a stable population of microglia takes up plasma proteins in a region-specific manner in healthy brains. To understand these two populations at the single cell transcriptomic level, we sorted plasma-positive microglia and plasma-negative microglia from hypothalamus region of young mice (3-month-old) and perform droplet-based scRNA-seq. Overall design: Single cell RNAseq of sorted microglia from hypothalamus region of young mice 20 hours after injecting with dye-labeled plasma protein (from multiple pooled mice), using 10x Genomics Drop-seq (v3.1). Microglia are identified as plasma-positive microglia or plasma-negative microglia during FACS sorting step.