Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia 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 microglia at the single cell transcriptomic level and correlate their transcriptome with plasma uptake intensity, we sorted plasma-high, plasma-low, and plasma-negative microglia from young mice (3-month-old) and perform plate-based scRNA-seq. Microglia are isolated from 3-month-old young mice, 20 hours after injecting NHS-Atto647N labeled plasma proteins. Based on the intensity of plasma protein within each cell, microglia were assigned into plasma negative (plasma-neg), plasma-low and plasma-high groups. The sorted microglia were then used to perform plate-based single-cell RNA sequencing (scRNA-seq) using smart-seq2 pipeline.